diff --git a/src/adapters/fileSystem.stub.ts b/src/adapters/fileSystem.stub.ts
index 678432b34..e10337f93 100644
--- a/src/adapters/fileSystem.stub.ts
+++ b/src/adapters/fileSystem.stub.ts
@@ -1,8 +1,9 @@
 import { FileSystem } from "../adapters/fileSystem";
 import { fn } from "../fn";
 
-export const createStubFileSystem = ({ data = {}, exists = true } = {}) => ({
+export const createStubFileSystem = ({ data = {}, exists = true, isDir = false } = {}) => ({
     fileExists: async () => exists,
+    directoryExists: async () => exists && isDir,
     readFile: async () => data,
     writeFile: fn<FileSystem["writeFile"]>(),
 });
diff --git a/src/adapters/fileSystem.ts b/src/adapters/fileSystem.ts
index 2b5f825da..08a9434b6 100644
--- a/src/adapters/fileSystem.ts
+++ b/src/adapters/fileSystem.ts
@@ -1,5 +1,6 @@
 export type FileSystem = {
     fileExists: (filePath: string) => Promise<boolean>;
-    readFile: (filePath: string) => Promise<Error | string>;
-    writeFile: (filePath: string, contents: string) => Promise<Error | undefined>;
+    directoryExists: (filePath: string) => Promise<boolean>;
+    readFile: (filePath: string) => Promise<NodeJS.ErrnoException | string>;
+    writeFile: (filePath: string, contents: string) => Promise<NodeJS.ErrnoException | undefined>;
 };
diff --git a/src/adapters/fsFileSystem.ts b/src/adapters/fsFileSystem.ts
index 7e29dfde0..774f2c201 100644
--- a/src/adapters/fsFileSystem.ts
+++ b/src/adapters/fsFileSystem.ts
@@ -11,6 +11,14 @@ export const fsFileSystem: FileSystem = {
             return false;
         }
     },
+    directoryExists: async (filePath: string) => {
+        try {
+            const stat = await fs.promises.stat(filePath);
+            return stat.isDirectory();
+        } catch (error) {
+            return false;
+        }
+    },
     readFile: async (filePath: string) => {
         try {
             return (await fs.promises.readFile(filePath)).toString();
diff --git a/src/api/dependencies.ts b/src/api/dependencies.ts
index 37269d04f..a9fd55454 100644
--- a/src/api/dependencies.ts
+++ b/src/api/dependencies.ts
@@ -121,6 +121,7 @@ export const findOriginalConfigurationsDependencies: FindOriginalConfigurationsD
 
 export const collectCommentFileNamesDependencies: CollectCommentFileNamesDependencies = {
     findTypeScriptConfiguration: bind(findTypeScriptConfiguration, findConfigurationDependencies),
+    fileSystem: fsFileSystem,
 };
 
 export const extractGlobPathsDependencies: ExtractGlobPathsDependencies = {
diff --git a/src/comments/collectCommentFileNames.test.ts b/src/comments/collectCommentFileNames.test.ts
index 137b0b233..010837c72 100644
--- a/src/comments/collectCommentFileNames.test.ts
+++ b/src/comments/collectCommentFileNames.test.ts
@@ -1,5 +1,7 @@
 import { describe, expect, it } from "@jest/globals";
 
+import { createStubFileSystem } from "../adapters/fileSystem.stub";
+import { fsFileSystem as fileSystem } from "../adapters/fsFileSystem";
 import { collectCommentFileNames } from "./collectCommentFileNames";
 
 const stubFoundConfiguration = {
@@ -10,7 +12,10 @@ describe("collectCommentFileNames", () => {
     it("returns an error result when filePathGlobs is true and typescriptConfiguration is undefined", async () => {
         const findTypeScriptConfiguration = async () => stubFoundConfiguration;
 
-        const result = await collectCommentFileNames({ findTypeScriptConfiguration }, true);
+        const result = await collectCommentFileNames(
+            { findTypeScriptConfiguration, fileSystem },
+            true,
+        );
 
         expect(result).toEqual(expect.any(Error));
     });
@@ -22,7 +27,7 @@ describe("collectCommentFileNames", () => {
         };
 
         const result = await collectCommentFileNames(
-            { findTypeScriptConfiguration },
+            { findTypeScriptConfiguration, fileSystem },
             true,
             typescriptConfiguration,
         );
@@ -35,7 +40,7 @@ describe("collectCommentFileNames", () => {
         const filePathGlobs = ["a.ts"];
 
         const result = await collectCommentFileNames(
-            { findTypeScriptConfiguration },
+            { findTypeScriptConfiguration, fileSystem },
             filePathGlobs,
         );
 
@@ -51,7 +56,7 @@ describe("collectCommentFileNames", () => {
         const filePathGlobs = "a.ts";
 
         const result = await collectCommentFileNames(
-            { findTypeScriptConfiguration },
+            { findTypeScriptConfiguration, fileSystem },
             filePathGlobs,
         );
 
@@ -65,7 +70,7 @@ describe("collectCommentFileNames", () => {
         const findTypeScriptConfiguration = async () => error;
 
         const result = await collectCommentFileNames(
-            { findTypeScriptConfiguration },
+            { findTypeScriptConfiguration, fileSystem },
             "tsconfig.json",
         );
 
@@ -76,7 +81,7 @@ describe("collectCommentFileNames", () => {
         const findTypeScriptConfiguration = async () => stubFoundConfiguration;
 
         const result = await collectCommentFileNames(
-            { findTypeScriptConfiguration },
+            { findTypeScriptConfiguration, fileSystem },
             "tsconfig.json",
         );
 
@@ -84,4 +89,22 @@ describe("collectCommentFileNames", () => {
             include: ["a.ts"],
         });
     });
+
+    it("returns only files when filePathGlobs includes directories", async () => {
+        const findTypeScriptConfiguration = async () => ({
+            include: ["directory"],
+        });
+
+        const result = await collectCommentFileNames(
+            {
+                findTypeScriptConfiguration,
+                fileSystem: createStubFileSystem({ isDir: true }),
+            },
+            "tsconfig.json",
+        );
+
+        expect(result).toEqual({
+            include: [],
+        });
+    });
 });
diff --git a/src/comments/collectCommentFileNames.ts b/src/comments/collectCommentFileNames.ts
index eef3e5860..570dcd5e2 100644
--- a/src/comments/collectCommentFileNames.ts
+++ b/src/comments/collectCommentFileNames.ts
@@ -1,3 +1,4 @@
+import { FileSystem } from "../adapters/fileSystem";
 import { SansDependencies } from "../binding";
 import {
     findTypeScriptConfiguration,
@@ -7,6 +8,7 @@ import { uniqueFromSources } from "../utils";
 
 export type CollectCommentFileNamesDependencies = {
     findTypeScriptConfiguration: SansDependencies<typeof findTypeScriptConfiguration>;
+    fileSystem: Pick<FileSystem, "directoryExists">;
 };
 
 export type CommentFileNames = {
@@ -26,12 +28,27 @@ export const collectCommentFileNames = async (
             );
         }
 
+        const includeList = uniqueFromSources(
+            typescriptConfiguration.files,
+            typescriptConfiguration.include,
+        );
+
+        // Remove directories specified in the include list. Ignore
+        // Errors as they'll be handled when reading the file.
+        const includeListFiles = (
+            await Promise.all(includeList.map(dependencies.fileSystem.directoryExists))
+        )
+            .map((isDirectory, i) => {
+                if (isDirectory) {
+                    return null;
+                }
+                return includeList[i];
+            })
+            .filter((item): item is string => typeof item === "string");
+
         return {
             exclude: typescriptConfiguration.exclude,
-            include: uniqueFromSources(
-                typescriptConfiguration.files,
-                typescriptConfiguration.include,
-            ),
+            include: includeListFiles,
         };
     }
 
diff --git a/src/converters/comments/convertFileComments.test.ts b/src/converters/comments/convertFileComments.test.ts
index 0e94c709d..24fa14a19 100644
--- a/src/converters/comments/convertFileComments.test.ts
+++ b/src/converters/comments/convertFileComments.test.ts
@@ -6,7 +6,7 @@ import { createStubConverter } from "../lintConfigs/rules/ruleConverter.stubs";
 import { convertFileComments, ConvertFileCommentsDependencies } from "./convertFileComments";
 
 const createStubDependencies = (
-    readFileResult: Error | string,
+    readFileResult: NodeJS.ErrnoException | string,
 ): ConvertFileCommentsDependencies => ({
     converters: new Map([
         ["ts-a", createStubConverter(["es-a"])],