diff --git a/bom/application/pom.xml b/bom/application/pom.xml
index b263319a471ec..f83445563a601 100644
--- a/bom/application/pom.xml
+++ b/bom/application/pom.xml
@@ -159,7 +159,7 @@
         <maven-invoker.version>3.2.0</maven-invoker.version>
         <awaitility.version>4.3.0</awaitility.version>
         <jboss-logmanager.version>3.1.2.Final</jboss-logmanager.version>
-        <flyway.version>11.15.0</flyway.version>
+        <flyway.version>11.16.0</flyway.version>
         <yasson.version>3.0.4</yasson.version>
         <!-- liquibase-mongodb is not released everytime with liquibase anymore, but the two versions need to be compatible -->
         <liquibase.version>4.33.0</liquibase.version>
diff --git a/extensions/flyway/runtime/src/main/java/io/quarkus/flyway/runtime/QuarkusPathLocationScanner.java b/extensions/flyway/runtime/src/main/java/io/quarkus/flyway/runtime/QuarkusPathLocationScanner.java
index 8d2b4dda36285..5fa43e3d1ab97 100644
--- a/extensions/flyway/runtime/src/main/java/io/quarkus/flyway/runtime/QuarkusPathLocationScanner.java
+++ b/extensions/flyway/runtime/src/main/java/io/quarkus/flyway/runtime/QuarkusPathLocationScanner.java
@@ -6,9 +6,11 @@
 import java.util.Collections;
 import java.util.Map;
 
+import org.flywaydb.core.api.CoreLocationPrefix;
 import org.flywaydb.core.api.Location;
 import org.flywaydb.core.api.callback.Callback;
 import org.flywaydb.core.api.configuration.Configuration;
+import org.flywaydb.core.api.locations.LocationParser;
 import org.flywaydb.core.api.migration.JavaMigration;
 import org.flywaydb.core.api.resource.LoadableResource;
 import org.flywaydb.core.internal.resource.classpath.ClassPathResource;
@@ -44,12 +46,13 @@ public QuarkusPathLocationScanner(Configuration configuration, Collection<Locati
                 LOGGER.debugf("Loading %s", migrationFile);
 
                 scannedResources.add(new ClassPathResource(null, migrationFile, classLoader, StandardCharsets.UTF_8));
-            } else if (migrationFile.startsWith(Location.FILESYSTEM_PREFIX)) {
+            } else if (migrationFile.startsWith(CoreLocationPrefix.FILESYSTEM_PREFIX)) {
                 if (fileSystemScanner == null) {
-                    fileSystemScanner = new FileSystemScanner(false, configuration);
+                    fileSystemScanner = new FileSystemScanner(configuration);
                 }
                 LOGGER.debugf("Checking %s for migration files", migrationFile);
-                Collection<LoadableResource> resources = fileSystemScanner.scanForResources(new Location(migrationFile));
+                Collection<LoadableResource> resources = fileSystemScanner
+                        .scanForResources(LocationParser.parseLocation(migrationFile));
                 LOGGER.debugf("%s contains %d migration files", migrationFile, resources.size());
                 scannedResources.addAll(resources);
             }
@@ -83,7 +86,7 @@ public Collection<LoadableResource> scanForResources() {
 
     private boolean isClassPathResource(Collection<Location> locations, String migrationFile) {
         for (Location location : locations) {
-            String locationPath = location.getPath();
+            String locationPath = location.getRootPath();
             if (!locationPath.endsWith(LOCATION_SEPARATOR)) {
                 locationPath += "/";
             }