diff --git a/docs/pages/release_notes.md b/docs/pages/release_notes.md
index 6726bc0659..8216e8aeeb 100644
--- a/docs/pages/release_notes.md
+++ b/docs/pages/release_notes.md
@@ -15,6 +15,8 @@ This is a {{ site.pmd.release_type }} release.
 ### New and noteworthy
 
 ### Fixed Issues
+* core
+    * [#3999](https://github.com/pmd/pmd/issues/3999): \[cli] All files are analyzed despite parameter `--file-list`
 * java-design
     * [#3981](https://github.com/pmd/pmd/issues/3981): \[java] ImmutableField reports fields annotated with @Value (Spring)
     * [#3998](https://github.com/pmd/pmd/issues/3998): \[java] ImmutableField reports fields annotated with @Captor (Mockito)
diff --git a/pmd-core/src/main/java/net/sourceforge/pmd/cli/PMDParameters.java b/pmd-core/src/main/java/net/sourceforge/pmd/cli/PMDParameters.java
index 18c1da8a28..6b1888db54 100644
--- a/pmd-core/src/main/java/net/sourceforge/pmd/cli/PMDParameters.java
+++ b/pmd-core/src/main/java/net/sourceforge/pmd/cli/PMDParameters.java
@@ -224,7 +224,7 @@ public class PMDParameters {
      */
     public PMDConfiguration toConfiguration() {
         PMDConfiguration configuration = new PMDConfiguration();
-        configuration.setInputPaths(this.getSourceDir());
+        configuration.setInputPaths(this.getInputPaths());
         configuration.setInputFilePath(this.getFileListPath());
         configuration.setIgnoreFilePath(this.getIgnoreListPath());
         configuration.setInputUri(this.getUri());
diff --git a/pmd-core/src/test/java/net/sourceforge/pmd/cli/PMDCommandLineInterfaceTest.java b/pmd-core/src/test/java/net/sourceforge/pmd/cli/PMDCommandLineInterfaceTest.java
index 5923717395..897884da7a 100644
--- a/pmd-core/src/test/java/net/sourceforge/pmd/cli/PMDCommandLineInterfaceTest.java
+++ b/pmd-core/src/test/java/net/sourceforge/pmd/cli/PMDCommandLineInterfaceTest.java
@@ -4,6 +4,8 @@
 
 package net.sourceforge.pmd.cli;
 
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
 
 import org.junit.Assert;
@@ -100,4 +102,15 @@ public class PMDCommandLineInterfaceTest {
         Assert.assertNotNull(PMDCommandLineInterface.buildUsageText());
     }
 
+    @Test
+    public void testOnlyFileListOption() {
+        PMDParameters params = new PMDParameters();
+        String[] args = {"--file-list", "pmd.filelist", "-f", "text", "-R", "rulesets/java/quickstart.xml", "--no-cache", };
+        PMDCommandLineInterface.extractParameters(params, args, "PMD");
+
+        PMDConfiguration config = params.toConfiguration();
+        assertEquals("pmd.filelist", config.getInputFilePath());
+        assertTrue(config.getAllInputPaths().isEmpty()); // no additional input paths
+        assertNull(config.getInputPaths());
+    }
 }