Call two different function.js depending on page

You can write conditionals in your functions.php file to conditionally load the javascript files. For example:

function theme_scripts() {
     // If this is the home page, run this script
     if(is_home()) {
         wp_enqueue_script( 'example-script', get_stylesheet_directory_uri().'/path/to/file.js');
     }
     // Otherwise, run this script
     else {
         wp_enqueue_script( 'other-script', get_stylesheet_directory_uri().'/path/to/file.js');
     }
}
add_action( 'wp_enqueue_scripts', 'theme_scripts' );

Codex page for home page conditional can be found here.
The Codex page for conditionals in general can be found here.
And you can find info on enqueuing scripts here.