Need to override block.tpl.php in a module
The following worked for me:

/**
 * Implements hook_theme().
 */
function rals_theme($existing, $type, $theme, $path) {
  $theme = array();
  $theme['block__custom'] = array(
    'render element' =&gt; 'content',
    'template' =&gt; 'block--custom',
    'path' =&gt; drupal_get_path('module', 'rals'),
   );
  return $theme;
}


/**
 * Implements hook_preprocess_HOOK().
 */
function rals_preprocess_block(&amp;$variables) {
  $block = $variables['block'];
  if ($block-&gt;bid == 3) {
    $variables['theme_hook_suggestions'][] = 'block__custom';
  }
}


and succesfully uses my module-folder-located template file for rendering the block with bid == 3.

Good luck in any case!