Within each group, the teams would play a double round-robin to decide their positions in the league.
The three group winners and the three runners-up, together with the two best third placed teams, then contested a play-off for the two promotion slots.
In advance of this season, FC Sion had been denied a licence by the Swiss Football Association (ASF-SFV) for the 2003–04 Challenge League and were, therefore, demoted to the amateur level.
Due to the settlement decision, the ASF-SFV were forced to withdraw the club from this division and to admit them to the Challenge League, the next highest tier.
From this moment, group 1 continued with just 15 teams and all results of the matches with Sion were voided.
Young Fellows Juventus win 5–3 on aggregate and are promoted to 2004–05 Challenge League.
Group 2 champions were [[SC Young Fellows Juventus]|Young Fellows Juventus]], runners-up were Basel U-21 but they were not eligible to the play-offs, this right was passed down to third placed Wangen b.O.. YFJ achieved promotion during the play-offs, but Wangen b.O.
Liga Interregional group winners and by Urania Genève Sport, who were the best placed runners-up.