diff --git a/src/API.jl b/src/API.jl
index 1adcbaef1f..49ae21936e 100644
--- a/src/API.jl
+++ b/src/API.jl
@@ -1046,18 +1046,33 @@ function gc(ctx::Context = Context(); collect_delay::Union{Period, Nothing} = no
         end
     end
 
-    # Delete any files that could not be rm-ed and were specially moved to the delayed delete directory.
-    # Do this silently because it's out of scope for Pkg.gc() but it's helpful to use this opportunity to do it
-    if isdefined(Base.Filesystem, :delayed_delete_dir)
-        if isdir(Base.Filesystem.delayed_delete_dir())
-            for p in readdir(Base.Filesystem.delayed_delete_dir(), join = true)
+    # Delete anything that could not be rm-ed and was specially recorded in the delayed delete reference folder.
+    # Do this silently because it's out of scope for Pkg.gc() but it's helpful to use this opportunity to do it.
+    if isdefined(Base.Filesystem, :delayed_delete_ref)
+        delayed_delete_ref_path = Base.Filesystem.delayed_delete_ref()
+        if isdir(delayed_delete_ref_path)
+            delayed_delete_dirs = Set{String}()
+            for f in readdir(delayed_delete_ref_path; join = true)
                 try
+                    p = readline(f)
+                    push!(delayed_delete_dirs, dirname(p))
                     Base.Filesystem.prepare_for_deletion(p)
                     Base.rm(p; recursive = true, force = true, allow_delayed_delete = false)
+                    Base.rm(f)
                 catch e
                     @debug "Failed to delete $p" exception = e
                 end
             end
+            for dir in delayed_delete_dirs
+                if basename(dir) == "julia_delayed_deletes" && isempty(readdir(dir))
+                    Base.Filesystem.prepare_for_deletion(dir)
+                    Base.rm(dir; recursive = true)
+                end
+            end
+            if isempty(readdir(delayed_delete_ref_path))
+                Base.Filesystem.prepare_for_deletion(delayed_delete_ref_path)
+                Base.rm(delayed_delete_ref_path; recursive = true)
+            end
         end
     end
 
diff --git a/test/pkg.jl b/test/pkg.jl
index 91206c93a7..07fe417a30 100644
--- a/test/pkg.jl
+++ b/test/pkg.jl
@@ -694,6 +694,27 @@ end
     end
 end
 
+if isdefined(Base.Filesystem, :delayed_delete_ref)
+    @testset "Pkg.gc for delayed deletes" begin
+        mktempdir() do root
+            dir = joinpath(root, "julia_delayed_deletes")
+            mkdir(dir)
+            testfile = joinpath(dir, "testfile")
+            write(testfile, "foo bar")
+            delayed_delete_ref_path = Base.Filesystem.delayed_delete_ref()
+            mkpath(delayed_delete_ref_path)
+            ref = tempname(delayed_delete_ref_path; cleanup = false)
+            write(ref, testfile)
+            @test isfile(testfile)
+            Pkg.gc()
+            @test !ispath(testfile)
+            @test !ispath(dir)
+            @test !ispath(ref)
+            @test !ispath(delayed_delete_ref_path) || !isempty(readdir(delayed_delete_ref_path))
+        end
+    end
+end
+
 #issue #876
 @testset "targets should survive add/rm" begin
     temp_pkg_dir() do project_path