diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5f521252af..e07439d13d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,8 @@ All notable changes to `src-cli` are documented in this file.
 
 ### Fixed
 
+- Fixes a nil-panic that could be caused when `src batch [preview|apply]` would encounter a repository that was currently being cloned or is empty.
+
 ### Removed
 
 ## 3.31.2
diff --git a/internal/batches/service/service.go b/internal/batches/service/service.go
index cb2b43500c..324dde1d81 100644
--- a/internal/batches/service/service.go
+++ b/internal/batches/service/service.go
@@ -12,6 +12,7 @@ import (
 	"strings"
 
 	"github.com/cockroachdb/errors"
+
 	batcheslib "github.com/sourcegraph/sourcegraph/lib/batches"
 
 	"github.com/sourcegraph/src-cli/internal/api"
@@ -431,19 +432,23 @@ func (svc *Service) ResolveRepositories(ctx context.Context, spec *batcheslib.Ba
 			return nil, errors.Wrapf(err, "resolving %q", on.String())
 		}
 
+		reposWithBranch := make([]*graphql.Repository, 0, len(repos))
+		for _, repo := range repos {
+			if !repo.HasBranch() {
+				continue
+			}
+			reposWithBranch = append(reposWithBranch, repo)
+		}
+
 		var repoBatchIgnores map[*graphql.Repository][]string
 		if !svc.allowIgnored {
-			repoBatchIgnores, err = svc.FindDirectoriesInRepos(ctx, ".batchignore", repos...)
+			repoBatchIgnores, err = svc.FindDirectoriesInRepos(ctx, ".batchignore", reposWithBranch...)
 			if err != nil {
 				return nil, err
 			}
 		}
 
-		for _, repo := range repos {
-			if !repo.HasBranch() {
-				continue
-			}
-
+		for _, repo := range reposWithBranch {
 			if other, ok := seen[repo.ID]; !ok {
 				seen[repo.ID] = repo
 
diff --git a/internal/batches/service/service_test.go b/internal/batches/service/service_test.go
index 44d0cfb021..5aa98aedaa 100644
--- a/internal/batches/service/service_test.go
+++ b/internal/batches/service/service_test.go
@@ -10,6 +10,7 @@ import (
 
 	"github.com/google/go-cmp/cmp"
 	"github.com/google/go-cmp/cmp/cmpopts"
+
 	batcheslib "github.com/sourcegraph/sourcegraph/lib/batches"
 
 	"github.com/sourcegraph/src-cli/internal/api"
@@ -322,6 +323,70 @@ const testBatchIgnoreInRepos = `{
 }
 `
 
+func TestResolveRepositories_RepoWithoutBranch(t *testing.T) {
+	spec := &batcheslib.BatchSpec{
+		On: []batcheslib.OnQueryOrRepository{
+			{RepositoriesMatchingQuery: "testquery"},
+		},
+	}
+
+	client, done := mockGraphQLClient(testResolveRepositoriesNoBranch, testBatchIgnoreInReposNoBranch)
+	defer done()
+
+	svc := &Service{client: client, allowIgnored: false}
+
+	repos, err := svc.ResolveRepositories(context.Background(), spec)
+	if err != nil {
+		t.Fatalf("unexpected error: %s", err)
+	}
+	if len(repos) != 1 {
+		t.Fatalf("wrong number of repos. want=%d, have=%d", 2, len(repos))
+	}
+}
+
+const testResolveRepositoriesNoBranch = `{
+  "data": {
+    "search": {
+      "results": {
+        "results": [
+          {
+            "__typename": "Repository",
+            "id": "UmVwb3NpdG9yeToxMw==",
+            "name": "bitbucket.sgdev.org/SOUR/automation-testing",
+            "url": "/bitbucket.sgdev.org/SOUR/automation-testing",
+            "externalRepository": { "serviceType": "bitbucketserver" },
+            "defaultBranch": null
+          },
+          {
+            "__typename": "Repository",
+            "id": "UmVwb3NpdG9yeTo0",
+            "name": "github.com/sourcegraph/automation-testing",
+            "url": "/github.com/sourcegraph/automation-testing",
+            "externalRepository": { "serviceType": "github" },
+            "defaultBranch": null
+          },
+          {
+            "__typename": "Repository",
+            "id": "UmVwb3NpdG9yeTo2MQ==",
+            "name": "gitlab.sgdev.org/sourcegraph/automation-testing",
+            "url": "/gitlab.sgdev.org/sourcegraph/automation-testing",
+            "externalRepository": { "serviceType": "gitlab" },
+            "defaultBranch": { "name": "refs/heads/master", "target": { "oid": "3b79a5d479d2af9cfe91e0aad4e9dddca7278150" } }
+          }
+        ]
+      }
+    }
+  }
+}
+`
+
+const testBatchIgnoreInReposNoBranch = `{
+    "data": {
+        "repo_0": { "results": { "results": [] } }
+    }
+}
+`
+
 func TestService_FindDirectoriesInRepos(t *testing.T) {
 	client, done := mockGraphQLClient(testFindDirectoriesInRepos)
 	defer done()