Override module's template in theme Suppose i have this hook_theme() in my module, choosing a template inside the module:
     

/**
 * Implements hook_theme().
 */
 function module_theme($existing, $type, $theme, $path) {
   return array(
     'module-output' =&gt; array(
       'template'  =&gt; 'output-template',
       'variables' =&gt; array(),
   ),
 }


If i put the same output-template.tpl.php inside my active theme, Drupal picks up the module's template.

Is there a way to make Drupal understand that if a template with the same filename exists somewhere in the theme, to pick the theme's template and not the module's (like an override)?
You can override tpl files defined in modules inside your active theme (under the templates directory). But Drupal will look for a file name using the defined theme key name and not the defined template file.

In your case, you should create a module-output.tpl.php file within your theme. Maybe a good practice to name your template file the same as your theme definition.