diff --git a/lib/jekyll/entry_filter.rb b/lib/jekyll/entry_filter.rb
index 49404a769be..787625e210a 100644
--- a/lib/jekyll/entry_filter.rb
+++ b/lib/jekyll/entry_filter.rb
@@ -28,20 +28,30 @@ def relative_to_source(entry)
       )
     end
 
+    # rubocop:disable Metrics/CyclomaticComplexity
     def filter(entries)
       entries.reject do |e|
         # Reject this entry if it is just a "dot" representation.
         #   e.g.: '.', '..', '_movies/.', 'music/..', etc
         next true if e.end_with?(".")
-        # Reject this entry if it is a symlink.
+
+        # Check if the current entry is explicitly included and cache the result
+        included = included?(e)
+
+        # Reject current entry if it is excluded but not explicitly included as well.
+        next true if excluded?(e) && !included
+
+        # Reject current entry if it is a symlink.
         next true if symlink?(e)
-        # Do not reject this entry if it is included.
-        next false if included?(e)
 
-        # Reject this entry if it is special, a backup file, or excluded.
-        special?(e) || backup?(e) || excluded?(e)
+        # Do not reject current entry if it is explicitly included.
+        next false if included
+
+        # Reject current entry if it is special or a backup file.
+        special?(e) || backup?(e)
       end
     end
+    # rubocop:enable Metrics/CyclomaticComplexity
 
     def included?(entry)
       glob_include?(site.include, entry) ||
diff --git a/test/test_entry_filter.rb b/test/test_entry_filter.rb
index 8d7b154d2ab..fc0dfeb2e9d 100644
--- a/test/test_entry_filter.rb
+++ b/test/test_entry_filter.rb
@@ -64,6 +64,16 @@ class TestEntryFilter < JekyllUnitTest
       assert_equal files, @site.reader.filter_entries(files)
     end
 
+    should "not exclude explicitly included entry" do
+      entries  = %w(README TODO css .htaccess _movies/.)
+      excludes = %w(README TODO css)
+      includes = %w(README .htaccess)
+      @site.exclude = excludes
+      @site.include = includes
+      filtered_entries = EntryFilter.new(@site).filter(entries)
+      assert_equal %w(README .htaccess), filtered_entries
+    end
+
     should "keep safe symlink entries when safe mode enabled" do
       allow(File).to receive(:symlink?).with("symlink.js").and_return(true)
       files = %w(symlink.js)