diff --git a/src/server/mcp.test.ts b/src/server/mcp.test.ts
index c4bc9c5a7..9bc40f316 100644
--- a/src/server/mcp.test.ts
+++ b/src/server/mcp.test.ts
@@ -227,6 +227,10 @@ describe('ResourceTemplate', () => {
 });
 
 describe('tool()', () => {
+    afterEach(() => {
+        jest.restoreAllMocks();
+    });
+
     /***
      * Test: Zero-Argument Tool Registration
      */
@@ -1692,6 +1696,56 @@ describe('tool()', () => {
         expect(result.tools[0].name).toBe('test-without-meta');
         expect(result.tools[0]._meta).toBeUndefined();
     });
+
+    test('should validate tool names according to SEP specification', () => {
+        // Create a new server instance for this test
+        const testServer = new McpServer({
+            name: 'test server',
+            version: '1.0'
+        });
+
+        // Spy on console.warn to verify warnings are logged
+        const warnSpy = jest.spyOn(console, 'warn').mockImplementation();
+
+        // Test valid tool names
+        testServer.registerTool(
+            'valid-tool-name',
+            {
+                description: 'A valid tool name'
+            },
+            async () => ({ content: [{ type: 'text' as const, text: 'Success' }] })
+        );
+
+        // Test tool name with warnings (starts with dash)
+        testServer.registerTool(
+            '-warning-tool',
+            {
+                description: 'A tool name that generates warnings'
+            },
+            async () => ({ content: [{ type: 'text' as const, text: 'Success' }] })
+        );
+
+        // Test invalid tool name (contains spaces)
+        testServer.registerTool(
+            'invalid tool name',
+            {
+                description: 'An invalid tool name'
+            },
+            async () => ({ content: [{ type: 'text' as const, text: 'Success' }] })
+        );
+
+        // Verify that warnings were issued (both for warnings and validation failures)
+        expect(warnSpy).toHaveBeenCalled();
+
+        // Verify specific warning content
+        const warningCalls = warnSpy.mock.calls.map(call => call.join(' '));
+        expect(warningCalls.some(call => call.includes('Tool name starts or ends with a dash'))).toBe(true);
+        expect(warningCalls.some(call => call.includes('Tool name contains spaces'))).toBe(true);
+        expect(warningCalls.some(call => call.includes('Tool name contains invalid characters'))).toBe(true);
+
+        // Clean up spies
+        warnSpy.mockRestore();
+    });
 });
 
 describe('resource()', () => {
diff --git a/src/server/mcp.ts b/src/server/mcp.ts
index 6593ea854..bee3b76ec 100644
--- a/src/server/mcp.ts
+++ b/src/server/mcp.ts
@@ -40,6 +40,7 @@ import { Completable, CompletableDef } from './completable.js';
 import { UriTemplate, Variables } from '../shared/uriTemplate.js';
 import { RequestHandlerExtra } from '../shared/protocol.js';
 import { Transport } from '../shared/transport.js';
+import { validateAndWarnToolName } from '../shared/toolNameValidation.js';
 
 /**
  * High-level MCP server that provides a simpler API for working with resources, tools, and prompts.
@@ -664,6 +665,9 @@ export class McpServer {
         _meta: Record<string, unknown> | undefined,
         callback: ToolCallback<ZodRawShape | undefined>
     ): RegisteredTool {
+        // Validate tool name according to SEP specification
+        validateAndWarnToolName(name);
+
         const registeredTool: RegisteredTool = {
             title,
             description,
@@ -678,6 +682,9 @@ export class McpServer {
             remove: () => registeredTool.update({ name: null }),
             update: updates => {
                 if (typeof updates.name !== 'undefined' && updates.name !== name) {
+                    if (typeof updates.name === 'string') {
+                        validateAndWarnToolName(updates.name);
+                    }
                     delete this._registeredTools[name];
                     if (updates.name) this._registeredTools[updates.name] = registeredTool;
                 }
diff --git a/src/shared/toolNameValidation.test.ts b/src/shared/toolNameValidation.test.ts
new file mode 100644
index 000000000..64ba9d3ba
--- /dev/null
+++ b/src/shared/toolNameValidation.test.ts
@@ -0,0 +1,127 @@
+import { validateToolName, validateAndWarnToolName, issueToolNameWarning } from './toolNameValidation.js';
+
+// Spy on console.warn to capture output
+let warnSpy: jest.SpyInstance;
+
+beforeEach(() => {
+    warnSpy = jest.spyOn(console, 'warn').mockImplementation();
+});
+
+afterEach(() => {
+    jest.restoreAllMocks();
+});
+
+describe('validateToolName', () => {
+    describe('valid tool names', () => {
+        test.each`
+            description                    | toolName
+            ${'simple alphanumeric names'} | ${'getUser'}
+            ${'names with underscores'}    | ${'get_user_profile'}
+            ${'names with dashes'}         | ${'user-profile-update'}
+            ${'names with dots'}           | ${'admin.tools.list'}
+            ${'mixed character names'}     | ${'DATA_EXPORT_v2.1'}
+            ${'single character names'}    | ${'a'}
+            ${'128 character names'}       | ${'a'.repeat(128)}
+        `('should accept $description', ({ toolName }) => {
+            const result = validateToolName(toolName);
+            expect(result.isValid).toBe(true);
+            expect(result.warnings).toHaveLength(0);
+        });
+    });
+
+    describe('invalid tool names', () => {
+        test.each`
+            description                            | toolName                  | expectedWarning
+            ${'empty names'}                       | ${''}                     | ${'Tool name cannot be empty'}
+            ${'names longer than 128 characters'}  | ${'a'.repeat(129)}        | ${'Tool name exceeds maximum length of 128 characters (current: 129)'}
+            ${'names with spaces'}                 | ${'get user profile'}     | ${'Tool name contains invalid characters: " "'}
+            ${'names with commas'}                 | ${'get,user,profile'}     | ${'Tool name contains invalid characters: ","'}
+            ${'names with forward slashes'}        | ${'user/profile/update'}  | ${'Tool name contains invalid characters: "/"'}
+            ${'names with other special chars'}    | ${'user@domain.com'}      | ${'Tool name contains invalid characters: "@"'}
+            ${'names with multiple invalid chars'} | ${'user name@domain,com'} | ${'Tool name contains invalid characters: " ", "@", ","'}
+            ${'names with unicode characters'}     | ${'user-ñame'}            | ${'Tool name contains invalid characters: "ñ"'}
+        `('should reject $description', ({ toolName, expectedWarning }) => {
+            const result = validateToolName(toolName);
+            expect(result.isValid).toBe(false);
+            expect(result.warnings).toContain(expectedWarning);
+        });
+    });
+
+    describe('warnings for potentially problematic patterns', () => {
+        test.each`
+            description                               | toolName              | expectedWarning                                                                            | shouldBeValid
+            ${'names with spaces'}                    | ${'get user profile'} | ${'Tool name contains spaces, which may cause parsing issues'}                             | ${false}
+            ${'names with commas'}                    | ${'get,user,profile'} | ${'Tool name contains commas, which may cause parsing issues'}                             | ${false}
+            ${'names starting with dash'}             | ${'-get-user'}        | ${'Tool name starts or ends with a dash, which may cause parsing issues in some contexts'} | ${true}
+            ${'names ending with dash'}               | ${'get-user-'}        | ${'Tool name starts or ends with a dash, which may cause parsing issues in some contexts'} | ${true}
+            ${'names starting with dot'}              | ${'.get.user'}        | ${'Tool name starts or ends with a dot, which may cause parsing issues in some contexts'}  | ${true}
+            ${'names ending with dot'}                | ${'get.user.'}        | ${'Tool name starts or ends with a dot, which may cause parsing issues in some contexts'}  | ${true}
+            ${'names with leading and trailing dots'} | ${'.get.user.'}       | ${'Tool name starts or ends with a dot, which may cause parsing issues in some contexts'}  | ${true}
+        `('should warn about $description', ({ toolName, expectedWarning, shouldBeValid }) => {
+            const result = validateToolName(toolName);
+            expect(result.isValid).toBe(shouldBeValid);
+            expect(result.warnings).toContain(expectedWarning);
+        });
+    });
+});
+
+describe('issueToolNameWarning', () => {
+    test('should output warnings to console.warn', () => {
+        const warnings = ['Warning 1', 'Warning 2'];
+        issueToolNameWarning('test-tool', warnings);
+
+        expect(warnSpy).toHaveBeenCalledTimes(6); // Header + 2 warnings + 3 guidance lines
+        const calls = warnSpy.mock.calls.map(call => call.join(' '));
+        expect(calls[0]).toContain('Tool name validation warning for "test-tool"');
+        expect(calls[1]).toContain('- Warning 1');
+        expect(calls[2]).toContain('- Warning 2');
+        expect(calls[3]).toContain('Tool registration will proceed, but this may cause compatibility issues.');
+        expect(calls[4]).toContain('Consider updating the tool name');
+        expect(calls[5]).toContain('See SEP: Specify Format for Tool Names');
+    });
+
+    test('should handle empty warnings array', () => {
+        issueToolNameWarning('test-tool', []);
+        expect(warnSpy).toHaveBeenCalledTimes(0);
+    });
+});
+
+describe('validateAndWarnToolName', () => {
+    test.each`
+        description                       | toolName              | expectedResult | shouldWarn
+        ${'valid names with warnings'}    | ${'-get-user-'}       | ${true}        | ${true}
+        ${'completely valid names'}       | ${'get-user-profile'} | ${true}        | ${false}
+        ${'invalid names with spaces'}    | ${'get user profile'} | ${false}       | ${true}
+        ${'empty names'}                  | ${''}                 | ${false}       | ${true}
+        ${'names exceeding length limit'} | ${'a'.repeat(129)}    | ${false}       | ${true}
+    `('should handle $description', ({ toolName, expectedResult, shouldWarn }) => {
+        const result = validateAndWarnToolName(toolName);
+        expect(result).toBe(expectedResult);
+
+        if (shouldWarn) {
+            expect(warnSpy).toHaveBeenCalled();
+        } else {
+            expect(warnSpy).not.toHaveBeenCalled();
+        }
+    });
+
+    test('should include space warning for invalid names with spaces', () => {
+        validateAndWarnToolName('get user profile');
+        const warningCalls = warnSpy.mock.calls.map(call => call.join(' '));
+        expect(warningCalls.some(call => call.includes('Tool name contains spaces'))).toBe(true);
+    });
+});
+
+describe('edge cases and robustness', () => {
+    test.each`
+        description                               | toolName          | shouldBeValid | expectedWarning
+        ${'names with only dots'}                 | ${'...'}          | ${true}       | ${'Tool name starts or ends with a dot, which may cause parsing issues in some contexts'}
+        ${'names with only dashes'}               | ${'---'}          | ${true}       | ${'Tool name starts or ends with a dash, which may cause parsing issues in some contexts'}
+        ${'names with only forward slashes'}      | ${'///'}          | ${false}      | ${'Tool name contains invalid characters: "/"'}
+        ${'names with mixed valid/invalid chars'} | ${'user@name123'} | ${false}      | ${'Tool name contains invalid characters: "@"'}
+    `('should handle $description', ({ toolName, shouldBeValid, expectedWarning }) => {
+        const result = validateToolName(toolName);
+        expect(result.isValid).toBe(shouldBeValid);
+        expect(result.warnings).toContain(expectedWarning);
+    });
+});
diff --git a/src/shared/toolNameValidation.ts b/src/shared/toolNameValidation.ts
new file mode 100644
index 000000000..fa96afde0
--- /dev/null
+++ b/src/shared/toolNameValidation.ts
@@ -0,0 +1,115 @@
+/**
+ * Tool name validation utilities according to SEP: Specify Format for Tool Names
+ *
+ * Tool names SHOULD be between 1 and 128 characters in length (inclusive).
+ * Tool names are case-sensitive.
+ * Allowed characters: uppercase and lowercase ASCII letters (A-Z, a-z), digits
+ * (0-9), underscore (_), dash (-), and dot (.).
+ * Tool names SHOULD NOT contain spaces, commas, or other special characters.
+ */
+
+/**
+ * Regular expression for valid tool names according to SEP-986 specification
+ */
+const TOOL_NAME_REGEX = /^[A-Za-z0-9._-]{1,128}$/;
+
+/**
+ * Validates a tool name according to the SEP specification
+ * @param name - The tool name to validate
+ * @returns An object containing validation result and any warnings
+ */
+export function validateToolName(name: string): {
+    isValid: boolean;
+    warnings: string[];
+} {
+    const warnings: string[] = [];
+
+    // Check length
+    if (name.length === 0) {
+        return {
+            isValid: false,
+            warnings: ['Tool name cannot be empty']
+        };
+    }
+
+    if (name.length > 128) {
+        return {
+            isValid: false,
+            warnings: [`Tool name exceeds maximum length of 128 characters (current: ${name.length})`]
+        };
+    }
+
+    // Check for specific problematic patterns (these are warnings, not validation failures)
+    if (name.includes(' ')) {
+        warnings.push('Tool name contains spaces, which may cause parsing issues');
+    }
+
+    if (name.includes(',')) {
+        warnings.push('Tool name contains commas, which may cause parsing issues');
+    }
+
+    // Check for potentially confusing patterns (leading/trailing dashes, dots, slashes)
+    if (name.startsWith('-') || name.endsWith('-')) {
+        warnings.push('Tool name starts or ends with a dash, which may cause parsing issues in some contexts');
+    }
+
+    if (name.startsWith('.') || name.endsWith('.')) {
+        warnings.push('Tool name starts or ends with a dot, which may cause parsing issues in some contexts');
+    }
+
+    // Check for invalid characters
+    if (!TOOL_NAME_REGEX.test(name)) {
+        const invalidChars = name
+            .split('')
+            .filter(char => !/[A-Za-z0-9._-]/.test(char))
+            .filter((char, index, arr) => arr.indexOf(char) === index); // Remove duplicates
+
+        warnings.push(
+            `Tool name contains invalid characters: ${invalidChars.map(c => `"${c}"`).join(', ')}`,
+            'Allowed characters are: A-Z, a-z, 0-9, underscore (_), dash (-), and dot (.)'
+        );
+
+        return {
+            isValid: false,
+            warnings
+        };
+    }
+
+    return {
+        isValid: true,
+        warnings
+    };
+}
+
+/**
+ * Issues warnings for non-conforming tool names
+ * @param name - The tool name that triggered the warnings
+ * @param warnings - Array of warning messages
+ */
+export function issueToolNameWarning(name: string, warnings: string[]): void {
+    if (warnings.length > 0) {
+        console.warn(`Tool name validation warning for "${name}":`);
+        for (const warning of warnings) {
+            console.warn(`  - ${warning}`);
+        }
+        console.warn('Tool registration will proceed, but this may cause compatibility issues.');
+        console.warn('Consider updating the tool name to conform to the MCP tool naming standard.');
+        console.warn(
+            'See SEP: Specify Format for Tool Names (https://github.com/modelcontextprotocol/modelcontextprotocol/issues/986) for more details.'
+        );
+    }
+}
+
+/**
+ * Validates a tool name and issues warnings for non-conforming names
+ * @param name - The tool name to validate
+ * @returns true if the name is valid, false otherwise
+ */
+export function validateAndWarnToolName(name: string): boolean {
+    const result = validateToolName(name);
+
+    // Always issue warnings for any validation issues (both invalid names and warnings)
+    issueToolNameWarning(name, result.warnings);
+
+    return result.isValid;
+}