diff --git a/src/compiler/utilities.ts b/src/compiler/utilities.ts
index 85a19df7f0694..51853695d5dad 100644
--- a/src/compiler/utilities.ts
+++ b/src/compiler/utilities.ts
@@ -2430,7 +2430,7 @@ namespace ts {
         }
     }
 
-    export function getExternalModuleName(node: AnyImportOrReExport | ImportTypeNode | ImportCall): Expression | undefined {
+    export function getExternalModuleName(node: AnyImportOrReExport | ImportTypeNode | ImportCall | ModuleDeclaration): Expression | undefined {
         switch (node.kind) {
             case SyntaxKind.ImportDeclaration:
             case SyntaxKind.ExportDeclaration:
@@ -2441,6 +2441,8 @@ namespace ts {
                 return isLiteralImportTypeNode(node) ? node.argument.literal : undefined;
             case SyntaxKind.CallExpression:
                 return node.arguments[0];
+            case SyntaxKind.ModuleDeclaration:
+                return node.name.kind === SyntaxKind.StringLiteral ? node.name : undefined;
             default:
                 return Debug.assertNever(node);
         }
@@ -4118,11 +4120,21 @@ namespace ts {
         return file.moduleName || getExternalModuleNameFromPath(host, file.fileName, referenceFile && referenceFile.fileName);
     }
 
+    function getCanonicalAbsolutePath(host: ResolveModuleNameResolutionHost, path: string) {
+        return host.getCanonicalFileName(getNormalizedAbsolutePath(path, host.getCurrentDirectory()));
+    }
+
     export function getExternalModuleNameFromDeclaration(host: ResolveModuleNameResolutionHost, resolver: EmitResolver, declaration: ImportEqualsDeclaration | ImportDeclaration | ExportDeclaration | ModuleDeclaration | ImportTypeNode): string | undefined {
         const file = resolver.getExternalModuleFileFromDeclaration(declaration);
         if (!file || file.isDeclarationFile) {
             return undefined;
         }
+        // If the declaration already uses a non-relative name, and is outside the common source directory, continue to use it
+        const specifier = getExternalModuleName(declaration);
+        if (specifier && isStringLiteralLike(specifier) && !pathIsRelative(specifier.text) &&
+            getCanonicalAbsolutePath(host, file.path).indexOf(getCanonicalAbsolutePath(host, ensureTrailingDirectorySeparator(host.getCommonSourceDirectory()))) === -1) {
+            return undefined;
+        }
         return getResolvedExternalModuleName(host, file);
     }
 
diff --git a/tests/baselines/reference/declarationEmitCommonSourceDirectoryDoesNotContainAllFiles.js b/tests/baselines/reference/declarationEmitCommonSourceDirectoryDoesNotContainAllFiles.js
new file mode 100644
index 0000000000000..cf0c04350a84d
--- /dev/null
+++ b/tests/baselines/reference/declarationEmitCommonSourceDirectoryDoesNotContainAllFiles.js
@@ -0,0 +1,44 @@
+//// [tests/cases/compiler/declarationEmitCommonSourceDirectoryDoesNotContainAllFiles.ts] ////
+
+//// [index.ts]
+export * from "./src/"
+//// [index.ts]
+export class B {}
+//// [index.ts]
+import { B } from "b";
+
+export default function () {
+	return new B();
+}
+//// [index.ts]
+export * from "./src/"
+
+
+
+//// [index.d.ts]
+declare module "src/index" {
+    import { B } from "b";
+    export default function (): B;
+}
+declare module "index" {
+    export * from "src/index";
+}
+
+
+//// [DtsFileErrors]
+
+
+dist/index.d.ts(2,23): error TS2307: Cannot find module 'b' or its corresponding type declarations.
+
+
+==== dist/index.d.ts (1 errors) ====
+    declare module "src/index" {
+        import { B } from "b";
+                          ~~~
+!!! error TS2307: Cannot find module 'b' or its corresponding type declarations.
+        export default function (): B;
+    }
+    declare module "index" {
+        export * from "src/index";
+    }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/declarationEmitCommonSourceDirectoryDoesNotContainAllFiles.symbols b/tests/baselines/reference/declarationEmitCommonSourceDirectoryDoesNotContainAllFiles.symbols
new file mode 100644
index 0000000000000..baa1d95cce7a9
--- /dev/null
+++ b/tests/baselines/reference/declarationEmitCommonSourceDirectoryDoesNotContainAllFiles.symbols
@@ -0,0 +1,16 @@
+=== /a/index.ts ===
+export * from "./src/"
+No type information for this code.=== /b/index.ts ===
+export * from "./src/"
+No type information for this code.=== /b/src/index.ts ===
+export class B {}
+>B : Symbol(B, Decl(index.ts, 0, 0))
+
+=== /a/src/index.ts ===
+import { B } from "b";
+>B : Symbol(B, Decl(index.ts, 0, 8))
+
+export default function () {
+	return new B();
+>B : Symbol(B, Decl(index.ts, 0, 8))
+}
diff --git a/tests/baselines/reference/declarationEmitCommonSourceDirectoryDoesNotContainAllFiles.types b/tests/baselines/reference/declarationEmitCommonSourceDirectoryDoesNotContainAllFiles.types
new file mode 100644
index 0000000000000..a0218c7fe7f81
--- /dev/null
+++ b/tests/baselines/reference/declarationEmitCommonSourceDirectoryDoesNotContainAllFiles.types
@@ -0,0 +1,17 @@
+=== /a/index.ts ===
+export * from "./src/"
+No type information for this code.=== /b/index.ts ===
+export * from "./src/"
+No type information for this code.=== /b/src/index.ts ===
+export class B {}
+>B : B
+
+=== /a/src/index.ts ===
+import { B } from "b";
+>B : typeof B
+
+export default function () {
+	return new B();
+>new B() : B
+>B : typeof B
+}
diff --git a/tests/cases/compiler/declarationEmitCommonSourceDirectoryDoesNotContainAllFiles.ts b/tests/cases/compiler/declarationEmitCommonSourceDirectoryDoesNotContainAllFiles.ts
new file mode 100644
index 0000000000000..17ccd6bdd7440
--- /dev/null
+++ b/tests/cases/compiler/declarationEmitCommonSourceDirectoryDoesNotContainAllFiles.ts
@@ -0,0 +1,18 @@
+// @declaration: true
+// @emitDeclarationOnly: true
+// @outFile: dist/index.d.ts
+// @currentDirectory: /a
+// @noImplicitReferences: true
+// @filename: /b/index.ts
+export * from "./src/"
+// @filename: /b/src/index.ts
+export class B {}
+// @filename: /a/src/index.ts
+import { B } from "b";
+
+export default function () {
+	return new B();
+}
+// @filename: /a/index.ts
+export * from "./src/"
+// @link: /b -> /a/node_modules/b
\ No newline at end of file