diff --git a/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration.java b/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration.java
index a227d45bdca4..596a712ad491 100644
--- a/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration.java
+++ b/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration.java
@@ -143,6 +143,7 @@ else if (flywayDataSource != null) {
 			return configuration.getDataSource();
 		}
 
+		@SuppressWarnings("deprecation")
 		private void checkLocationExists(DataSource dataSource, FlywayProperties properties,
 				ResourceLoader resourceLoader) {
 			if (properties.isCheckLocation()) {
diff --git a/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayMigrationScriptMissingException.java b/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayMigrationScriptMissingException.java
index 4ac622585c77..76e5a4a7d67e 100644
--- a/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayMigrationScriptMissingException.java
+++ b/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayMigrationScriptMissingException.java
@@ -25,7 +25,9 @@
  * @author Anand Shastri
  * @author Stephane Nicoll
  * @since 2.2.0
+ * @deprecated since 2.5.0 as location checking is deprecated
  */
+@Deprecated
 public class FlywayMigrationScriptMissingException extends RuntimeException {
 
 	private final List<String> locations;
diff --git a/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayProperties.java b/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayProperties.java
index 1d4adb815236..9e42caf922f2 100644
--- a/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayProperties.java
+++ b/spring-boot-project/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/flyway/FlywayProperties.java
@@ -26,6 +26,7 @@
 import java.util.Map;
 
 import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.boot.context.properties.DeprecatedConfigurationProperty;
 
 /**
  * Configuration properties for Flyway database migrations.
@@ -45,8 +46,10 @@ public class FlywayProperties {
 	private boolean enabled = true;
 
 	/**
-	 * Whether to check that migration scripts location exists.
+	 * Whether to check that migration scripts location exists. Should be set to false
+	 * when using a wildcard location or a remote-hosted location such as S3 or GCS.
 	 */
+	@Deprecated
 	private boolean checkLocation = true;
 
 	/**
@@ -365,10 +368,14 @@ public void setEnabled(boolean enabled) {
 		this.enabled = enabled;
 	}
 
+	@Deprecated
+	@DeprecatedConfigurationProperty(
+			reason = "Locations can no longer be checked accurately due to changes in Flyway's location support.")
 	public boolean isCheckLocation() {
 		return this.checkLocation;
 	}
 
+	@Deprecated
 	public void setCheckLocation(boolean checkLocation) {
 		this.checkLocation = checkLocation;
 	}