diff --git a/mesonbuild/backend/ninjabackend.py b/mesonbuild/backend/ninjabackend.py
index f10d5164b..222e01dc8 100644
--- a/mesonbuild/backend/ninjabackend.py
+++ b/mesonbuild/backend/ninjabackend.py
@@ -560,6 +560,8 @@ int dummy;
         elif isinstance(texe, build.CustomTarget):
             deps.append(self.get_target_filename(texe))
             cmd += [os.path.join(self.environment.get_build_dir(), self.get_target_filename(texe))]
+        elif isinstance(texe, mesonlib.File):
+            cmd.append(texe.absolute_path(self.environment.get_source_dir(), self.environment.get_build_dir()))
         else:
             cmd.append(target.command)
         cmd += arg_strings
diff --git a/test cases/common/58 run target/configure.in b/test cases/common/58 run target/configure.in
new file mode 100755
index 000000000..0d42d0441
--- /dev/null
+++ b/test cases/common/58 run target/configure.in	
@@ -0,0 +1,3 @@
+#!/usr/bin/env python3
+
+print('Success')
\ No newline at end of file
diff --git a/test cases/common/58 run target/meson.build b/test cases/common/58 run target/meson.build
index a1c5ad8ab..686db1f81 100644
--- a/test cases/common/58 run target/meson.build	
+++ b/test cases/common/58 run target/meson.build	
@@ -49,3 +49,14 @@ run_target('check_exists',
 # executable but test that the output is generated correctly.
 run_target('donotrunme',
   command : hex)
+
+# Ensure configure files can be passed
+conf = configure_file(
+  input: 'configure.in',
+  output: 'configure',
+  configuration: configuration_data()
+)
+
+run_target('configure_script',
+  command : conf
+)