diff --git a/flang/CMakeLists.txt b/flang/CMakeLists.txt
--- a/flang/CMakeLists.txt
+++ b/flang/CMakeLists.txt
@@ -180,7 +180,7 @@
          ${LLVM_INCLUDE_TESTS})
   set(FLANG_GTEST_AVAIL 1)
 
-  set(FLANG_BINARY_DIR ${CMAKE_BINARY_DIR}/tools/flang)
+  set(FLANG_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR})
   set(BACKEND_PACKAGE_STRING "${PACKAGE_STRING}")
   if (LINK_WITH_FIR)
     set(MLIR_MAIN_SRC_DIR ${LLVM_MAIN_SRC_DIR}/../mlir/include ) # --src-root
@@ -194,8 +194,6 @@
 
 if(LINK_WITH_FIR)
   # tco tool and FIR lib output directories
-  set(LLVM_RUNTIME_OUTPUT_INTDIR ${CMAKE_BINARY_DIR}/bin)
-  set(LLVM_LIBRARY_OUTPUT_INTDIR ${CMAKE_BINARY_DIR}/lib)
   # Always build tco tool
   set(LLVM_BUILD_TOOLS ON)
   message(STATUS "Linking driver with FIR and LLVM")
diff --git a/flang/test/lit.cfg.py b/flang/test/lit.cfg.py
--- a/flang/test/lit.cfg.py
+++ b/flang/test/lit.cfg.py
@@ -61,7 +61,7 @@
     extra_args=["-intrinsic-module-directory "+config.flang_intrinsic_modules_dir],
     unresolved='fatal')
 ]
-llvm_config.add_tool_substitutions(tools, [config.flang_llvm_tools_dir])
+llvm_config.add_tool_substitutions(tools, config.llvm_tools_dir)
 
 # Enable libpgmath testing
 result = lit_config.params.get("LIBPGMATH")
diff --git a/flang/test/lit.site.cfg.py.in b/flang/test/lit.site.cfg.py.in
--- a/flang/test/lit.site.cfg.py.in
+++ b/flang/test/lit.site.cfg.py.in
@@ -7,7 +7,7 @@
 config.flang_src_dir = "@FLANG_SOURCE_DIR@"
 config.flang_tools_dir = "@FLANG_TOOLS_DIR@"
 config.flang_intrinsic_modules_dir = "@FLANG_INTRINSIC_MODULES_DIR@"
-config.flang_llvm_tools_dir = "@CMAKE_BINARY_DIR@/bin"
+config.flang_llvm_tools_dir = "@LLVM_TOOLS_DIR@"
 config.python_executable = "@PYTHON_EXECUTABLE@"
 
 # Support substitution of the tools_dir with user parameters. This is
diff --git a/flang/tools/f18/CMakeLists.txt b/flang/tools/f18/CMakeLists.txt
--- a/flang/tools/f18/CMakeLists.txt
+++ b/flang/tools/f18/CMakeLists.txt
@@ -59,8 +59,14 @@
 install(TARGETS f18 DESTINATION bin)
 
 set(FLANG_INTRINSIC_MODULES_DIR ${FLANG_BINARY_DIR}/include/flang)
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/flang.sh.in ${CMAKE_BINARY_DIR}/tools/flang/bin/flang @ONLY)
-file(COPY ${CMAKE_BINARY_DIR}/tools/flang/bin/flang DESTINATION ${CMAKE_BINARY_DIR}/bin FILE_PERMISSIONS OWNER_EXECUTE OWNER_READ OWNER_WRITE)
+# This flang shell script will only work in a POSIX shell.
+if (NOT WIN32)
+  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/flang.sh.in ${CMAKE_CURRENT_BINARY_DIR}/tools/flang/bin/flang @ONLY)
+add_custom_command(TARGET f18
+  POST_BUILD
+  COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_BINARY_DIR}/tools/flang/bin/flang ${LLVM_RUNTIME_OUTPUT_INTDIR}/flang
+  COMMAND chmod +x ${LLVM_RUNTIME_OUTPUT_INTDIR}/flang)
+endif()
 # The flang script to be installed needs a different path to the headers.
 set(FLANG_INTRINSIC_MODULES_DIR ${CMAKE_INSTALL_PREFIX}/include/flang)
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/flang.sh.in ${FLANG_BINARY_DIR}/bin/flang-install.sh @ONLY)