diff --git a/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration.java b/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration.java
index 014792bdd49..96c33a01a37 100644
--- a/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration.java
+++ b/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration.java
@@ -58,6 +58,7 @@ import org.springframework.util.ObjectUtils;
  * @author Phillip Webb
  * @author Vedran Pavic
  * @author Stephane Nicoll
+ * @author Jacques-Etienne Beaudet
  * @since 1.1.0
  */
 @Configuration
@@ -132,6 +133,9 @@ public class FlywayAutoConfiguration {
 			else {
 				flyway.setDataSource(this.dataSource);
 			}
+			// TODO: remove this line once SPR-13749 is fixed
+			flyway.setLocations(this.properties.getLocations().toArray(new String[0]));
+
 			return flyway;
 		}
 
diff --git a/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayProperties.java b/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayProperties.java
index b4dca435b98..b80d4327b73 100644
--- a/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayProperties.java
+++ b/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayProperties.java
@@ -16,6 +16,7 @@
 
 package org.springframework.boot.autoconfigure.flyway;
 
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
@@ -39,7 +40,7 @@ public class FlywayProperties {
 	/**
 	 * Locations of migrations scripts.
 	 */
-	private List<String> locations = Arrays.asList("db/migration");
+	private List<String> locations = new ArrayList<String>(Arrays.asList("db/migration"));
 
 	/**
 	 * Check that migration scripts location exists.
diff --git a/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfigurationTests.java b/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfigurationTests.java
index 86d5befcb10..37da00e6ca1 100644
--- a/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfigurationTests.java
+++ b/spring-boot-autoconfigure/src/test/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfigurationTests.java
@@ -130,6 +130,19 @@ public class FlywayAutoConfigurationTests {
 				Arrays.asList(flyway.getLocations()).toString());
 	}
 
+	@Test
+	public void overrideLocationsList() throws Exception {
+		EnvironmentTestUtils.addEnvironment(this.context,
+				"flyway.locations[0]:classpath:db/changelog",
+				"flyway.locations[1]:classpath:db/migration");
+		registerAndRefresh(EmbeddedDataSourceConfiguration.class,
+				FlywayAutoConfiguration.class,
+				PropertyPlaceholderAutoConfiguration.class);
+		Flyway flyway = this.context.getBean(Flyway.class);
+		assertEquals("[classpath:db/changelog, classpath:db/migration]",
+				Arrays.asList(flyway.getLocations()).toString());
+	}
+
 	@Test
 	public void overrideSchemas() throws Exception {
 		EnvironmentTestUtils.addEnvironment(this.context, "flyway.schemas:public");