diff --git a/tool/sync_default_gems.rb b/tool/sync_default_gems.rb
index 35246e56c84..2232f5ac88d 100755
--- a/tool/sync_default_gems.rb
+++ b/tool/sync_default_gems.rb
@@ -6,6 +6,7 @@ require 'fileutils'
 require "rbconfig"
 require "find"
 require "tempfile"
+require_relative "../lib/mkmf/depend"
 
 module SyncDefaultGems
   include FileUtils
@@ -46,7 +47,6 @@ module SyncDefaultGems
 
   def repo((upstream, branch), mappings, exclude: [])
     branch ||= CLASSICAL_DEFAULT_BRANCH
-    exclude += ["ext/**/depend"]
     Repository.new(upstream:, branch:, mappings:, exclude:)
   end
 
@@ -194,7 +194,6 @@ module SyncDefaultGems
       ["History.md", "ext/openssl/History.md"],
     ], exclude: [
       "test/openssl/envutil.rb",
-      "ext/openssl/depend",
     ]),
     optparse: lib("ruby/optparse", gemspec_in_subdir: true).tap {
       it.mappings << ["doc/optparse", "doc/optparse"]
@@ -395,6 +394,23 @@ module SyncDefaultGems
     end
   end
 
+  def minimize_dependencies(gem)
+    files = REPOSITORIES[gem].mappings.flat_map do |_src, dst|
+      if File.file?(dst)
+        File.basename(dst) == "depend" ? [dst] : []
+      elsif File.directory?(dst)
+        Dir.glob("#{dst}/**/depend")
+      else
+        []
+      end
+    end.uniq
+    return if files.empty?
+
+    MakeMakefile::Depend.new(root: Dir.pwd).run(
+      files, mode: :inplace, sources: true,
+    )
+  end
+
   # We usually don't use this. Please consider using #sync_default_gems_with_commits instead.
   def sync_default_gems(gem)
     config = REPOSITORIES[gem]
@@ -438,6 +454,7 @@ module SyncDefaultGems
     if gem == "rubygems"
       rubygems_do_fixup
     end
+    minimize_dependencies(gem)
 
     check_prerelease_version(gem)
 
@@ -653,6 +670,7 @@ module SyncDefaultGems
       if gem == "rubygems"
         rubygems_do_fixup
       end
+      minimize_dependencies(gem)
       replace_rdoc_ref_all_full
     end
 
diff --git a/tool/test/test_sync_default_gems.rb b/tool/test/test_sync_default_gems.rb
index b527b07ff8d..cf65173c3e8 100755
--- a/tool/test/test_sync_default_gems.rb
+++ b/tool/test/test_sync_default_gems.rb
@@ -225,6 +225,33 @@ module Test_SyncDefaultGems
       assert_operator(top_commit(@target), :start_with?, log.last[/\h+$/], out)
     end
 
+    def test_minimize_dependencies
+      SyncDefaultGems::REPOSITORIES[@target].mappings <<
+        ["ext/example", "ext/example"]
+      Dir.mkdir("#@target/ext")
+      Dir.mkdir("#@target/ext/example")
+      File.write("#@target/ext/example/example.c", <<~C)
+        #include "example.h"
+      C
+      File.write("#@target/ext/example/example.h", "")
+      File.write("#@target/ext/example/depend", <<~MAKE)
+        # AUTOGENERATED DEPENDENCIES START
+        example.o: example.c
+        example.o: example.h
+        # AUTOGENERATED DEPENDENCIES END
+      MAKE
+      git(*%W"add ext/example", chdir: @target)
+      git(*%W"commit -q -m", "Add extension", chdir: @target)
+
+      out = assert_sync()
+
+      assert_equal(<<~MAKE, File.read("src/ext/example/depend"), out)
+        # AUTOGENERATED DEPENDENCIES START
+        example.o: example.c
+        # AUTOGENERATED DEPENDENCIES END
+      MAKE
+    end
+
     def test_unknown_repository
       assert_raise_with_message(RuntimeError, /unknown/) do
         SyncDefaultGems::REPOSITORIES["not-exist"]