Source: Swiss Challenge League(in German) Rules for classification: 1) points; 2) goal difference; 3) number of goals scored. (C) Champions; (D) Disqualified; (R) Relegated Notes:
^Due to financial irregularities, AC Bellinzona was discounted seven points and were ultimately relegated at the end of the season. FC Locarno was thus not relegated in spite of their last-place finish.
The winners of the Semi-finals stage played in the final and the winners of the first semi-final in the draw were considered as home team for the final. In this FC Basel beat FC Sion 1−0. In the second semi-final Grasshoppers Zürich beat their local rivals FC Zürich 2−1 after extra time. The final was held on Whit Monday 20 May a2013 t the Stade de Suisse, Wankdorf.