diff --git a/core/config/filters.js b/core/config/filters.js
index bd33d10edcf9..c6fa3cfcf759 100644
--- a/core/config/filters.js
+++ b/core/config/filters.js
@@ -287,6 +287,12 @@ function filterConfigByGatherMode(resolvedConfig, mode) {
  */
 function filterConfigByExplicitFilters(resolvedConfig, filters) {
   const {onlyAudits, onlyCategories, skipAudits} = filters;
+  if (onlyAudits && !onlyAudits.length) {
+    throw new Error(`onlyAudits cannot be an empty array.`);
+  }
+  if (onlyCategories && !onlyCategories.length) {
+    throw new Error(`onlyCategories cannot be an empty array.`);
+  }
 
   warnOnUnknownOnlyCategories(resolvedConfig.categories, onlyCategories);
 
diff --git a/core/test/config/filters-test.js b/core/test/config/filters-test.js
index d46ea3f05133..aef68a95d020 100644
--- a/core/test/config/filters-test.js
+++ b/core/test/config/filters-test.js
@@ -634,5 +634,31 @@ describe('Fraggle Rock Config Filtering', () => {
         artifacts: [{id: 'Snapshot'}, {id: 'Timespan'}],
       });
     });
+
+    it('should not allow to pass an empty array to onlyAudits', () => {
+      resolvedConfig = {
+        ...resolvedConfig,
+      };
+      expect(() => {
+        filters.filterConfigByExplicitFilters(resolvedConfig, {
+          onlyAudits: [],
+          onlyCategories: null,
+          skipAudits: null,
+        });
+      }).toThrow('onlyAudits cannot be an empty array.');
+    });
+
+    it('should not allow to pass an empty array to onlyCategories', () => {
+      resolvedConfig = {
+        ...resolvedConfig,
+      };
+      expect(() => {
+        filters.filterConfigByExplicitFilters(resolvedConfig, {
+          onlyAudits: null,
+          onlyCategories: [],
+          skipAudits: null,
+        });
+      }).toThrow('onlyCategories cannot be an empty array.');
+    });
   });
 });