diff --git a/src/Bundle.js b/src/Bundle.js
index a050de2..0b7902f 100644
--- a/src/Bundle.js
+++ b/src/Bundle.js
@@ -15,7 +15,7 @@ import transformBundle from './utils/transformBundle.js';
 import collapseSourcemaps from './utils/collapseSourcemaps.js';
 import SOURCEMAPPING_URL from './utils/sourceMappingURL.js';
 import callIfFunction from './utils/callIfFunction.js';
-import { dirname, isRelative, relative, resolve } from './utils/path.js';
+import { dirname, isRelative, isAbsolute, relative, resolve } from './utils/path.js';
 
 export default class Bundle {
 	constructor ( options ) {
@@ -207,7 +207,12 @@ export default class Bundle {
 							if ( isRelative( source ) ) throw new Error( `Could not resolve ${source} from ${module.id}` );
 							if ( !~this.external.indexOf( source ) ) this.onwarn( `Treating '${source}' as external dependency` );
 						} else if ( resolvedId ) {
-							normalizedExternal = this.getPathRelativeToEntryDirname( resolvedId );
+							if ( isRelative(resolvedId) || isAbsolute(resolvedId) ) {
+								// Try to deduce relative path from entry dir if resolvedId is defined as a relative path.
+								normalizedExternal = this.getPathRelativeToEntryDirname( resolvedId );
+							} else {
+								normalizedExternal = resolvedId;
+							}
 						}
 						module.resolvedIds[ source ] = normalizedExternal;
 
diff --git a/test/function/external-alias/_config.js b/test/function/external-alias/_config.js
new file mode 100644
index 0000000..3232f3b
--- /dev/null
+++ b/test/function/external-alias/_config.js
@@ -0,0 +1,28 @@
+var assert = require( 'assert' );
+var path = require( 'path' );
+
+module.exports = {
+	description: 'includes an external module included dynamically by an alias',
+	options: {
+		entry: path.join( __dirname, 'first', 'main.js' ),
+		external: [ 'lodash' ],
+
+		// Define a simple alias plugin for underscore
+		plugins: [
+			{
+				resolveId: function ( id ) {
+					if ( id === 'underscore' ) {
+						return 'lodash';
+					}
+				}
+			}
+		]
+	},
+
+	context: {
+		require: function ( required ) {
+			assert.equal( required, 'lodash' );
+			return 1;
+		}
+	}
+};
diff --git a/test/function/external-alias/first/main.js b/test/function/external-alias/first/main.js
new file mode 100644
index 0000000..3503622
--- /dev/null
+++ b/test/function/external-alias/first/main.js
@@ -0,0 +1,10 @@
+import _ from 'underscore';
+import first from './module';
+
+export default function ( inputs ) {
+	if ( !_.isArray( inputs ) ) {
+		return inputs;
+	}
+
+	return first.square( inputs );
+};
diff --git a/test/function/external-alias/first/module.js b/test/function/external-alias/first/module.js
new file mode 100644
index 0000000..4bacbea
--- /dev/null
+++ b/test/function/external-alias/first/module.js
@@ -0,0 +1,7 @@
+import _ from 'underscore';
+
+export default function square ( inputs ) {
+	return _.map( inputs, function ( x ) {
+		return x * x;
+	});
+};