Create pagination in theme('table') when not using SQL query
Try the following function:

/**
 * An generic array pager for Drupal.
 * For Drupal 5 and 6, the default limit is 10. For Drupal 7 it is 9.
 */
function pager_array_splice($data, $limit = 9, $element = 0) {
  global $pager_page_array, $pager_total, $pager_total_items;
  $page = isset($_GET['page']) ? $_GET['page'] : '';

  // Convert comma-separated $page to an array, used by other functions.
  $pager_page_array = explode(',', $page);

  // We calculate the total of pages as ceil(items / limit).
  $pager_total_items[$element] = count($data);
  $pager_total[$element] = ceil($pager_total_items[$element] / $limit);
  $pager_page_array[$element] = max(0, min((int)$pager_page_array[$element], ((int)$pager_total[$element]) - 1));
  return array_slice($data, $pager_page_array[$element] * $limit, $limit, TRUE);
}

$output = pager_array_splice($yourarray, 5);  // 5 is per page values


See Paging non-SQL data for more details.