diff --git a/mesonbuild/backend/ninjabackend.py b/mesonbuild/backend/ninjabackend.py
index 16962a4b1..0a1681fc7 100644
--- a/mesonbuild/backend/ninjabackend.py
+++ b/mesonbuild/backend/ninjabackend.py
@@ -19,7 +19,7 @@ import pickle
 import subprocess
 from collections import OrderedDict
 import itertools
-from pathlib import PurePath
+from pathlib import PurePath, Path
 from functools import lru_cache
 
 from . import backends
@@ -1851,9 +1851,11 @@ rule FORTRAN_DEP_HACK%s
         mod_files = []
         usere = re.compile(r"\s*use,?\s*(?:non_intrinsic)?\s*(?:::)?\s*(\w+)", re.IGNORECASE)
         submodre = re.compile(r"\s*\bsubmodule\b\s+\((\w+:?\w+)\)\s+(\w+)\s*$", re.IGNORECASE)
-        dirname = self.get_target_private_dir(target)
+        dirname = Path(self.get_target_private_dir(target))
         tdeps = self.fortran_deps[target.get_basename()]
-        with open(src, encoding='ascii', errors='ignore') as f:
+        src = Path(src)
+        srcdir = Path(self.source_dir)
+        with src.open(encoding='ascii', errors='ignore') as f:
             for line in f:
                 usematch = usere.match(line)
                 if usematch is not None:
@@ -1876,10 +1878,14 @@ rule FORTRAN_DEP_HACK%s
                     # Check if a source uses a module it exports itself.
                     # Potential bug if multiple targets have a file with
                     # the same name.
-                    if mod_source_file.fname == os.path.basename(src):
-                        continue
+                    try:
+                        if (srcdir / mod_source_file.fname).samefile(src):
+                            continue
+                    except FileNotFoundError:
+                        pass
+
                     mod_name = compiler.module_name_to_filename(usename)
-                    mod_files.append(os.path.join(dirname, mod_name))
+                    mod_files.append(str(dirname / mod_name))
                 else:
                     submodmatch = submodre.match(line)
                     if submodmatch is not None:
@@ -1890,10 +1896,14 @@ rule FORTRAN_DEP_HACK%s
                         for parent in parents:
                             if parent not in tdeps:
                                 raise MesonException("submodule {} relies on parent module {} that was not found.".format(submodmatch.group(2).lower(), parent))
-                            if tdeps[parent].fname == os.path.basename(src):  # same file
-                                continue
+
+                            try:
+                                if (srcdir / tdeps[parent].fname).samefile(src):
+                                    continue
+                            except FileNotFoundError:
+                                pass
                             mod_name = compiler.module_name_to_filename(parent)
-                            mod_files.append(os.path.join(dirname, mod_name))
+                            mod_files.append(str(dirname / mod_name))
 
         return mod_files
 
diff --git a/test cases/fortran/4 self dependency/meson.build b/test cases/fortran/4 self dependency/meson.build
index bc5dab4ed..8eef4eb66 100644
--- a/test cases/fortran/4 self dependency/meson.build	
+++ b/test cases/fortran/4 self dependency/meson.build	
@@ -2,3 +2,5 @@ project('selfdep', 'fortran')
 
 e = executable('selfdep', 'selfdep.f90')
 test('selfdep', e)
+
+library('selfmod', 'src/selfdep_mod.f90')
diff --git a/test cases/fortran/4 self dependency/src/selfdep_mod.f90 b/test cases/fortran/4 self dependency/src/selfdep_mod.f90
new file mode 100644
index 000000000..4aa00576a
--- /dev/null
+++ b/test cases/fortran/4 self dependency/src/selfdep_mod.f90	
@@ -0,0 +1,6 @@
+module a
+end module a
+
+module b
+use a
+end module b
diff --git a/test cases/fortran/7 generated/prog.f90 b/test cases/fortran/7 generated/prog.f90
index c476e9c91..8a102c059 100644
--- a/test cases/fortran/7 generated/prog.f90	
+++ b/test cases/fortran/7 generated/prog.f90	
@@ -1,9 +1,7 @@
 program prog
-  use mod2
-  implicit none
+use mod2
+implicit none
 
-  if (modval1 + modval2 /= 3) then
-    stop 1
-  end if
+if (modval1 + modval2 /= 3) stop 1
 
 end program prog