| Competition: | 1. Liga |
| Season: | 1998–99 |
| Winners: | Overall Bellinzona Group 1: Echallens Group 2: Fribourg Group 3: Bellinzona Group 4: Winterthur |
| Promoted: | Winterthur Bellinzona |
| Relegated: | Group 1: Monthey FC Bramois Montreux-Sports Group 2: FC Riehen Köniz Group 3: Biaschesi FC Muri Group 4: SC Veltheim FC Wetzikon |
| Matches: | 4 times 182 plus 12 play-offs and 4 play-outs |
| Prevseason: | 1997–98 |
| Nextseason: | 1999–2000 |
The 1998–1999 Swiss 1. Liga was the 67th season of this league since its creation in 1931. At this time, the 1. Liga was the third tier of the Swiss football league system and it was the highest level of amateur football.
There were 56 clubs in the 1. Liga, divided into four regional groups of 14 teams. Within each group, the teams would play a double round-robin to decide their league position. The four group winners and the four runners-up then contested a play-off for the two promotion slots. The two last placed teams in each group were directly relegated to the 2. Liga Interregional (fourth tier). The four third-last placed teams would compete a play-out against the ninth relegation place.
| Club | Canton | Stadium | Capacity |
|---|---|---|---|
| FC Bex | Vaud | Relais | |
| FC Bramois[1] | Valais | Stade du Bois-de-la-Borgne/Glareys | |
| CS Chênois | Geneva | Stade des Trois-Chêne | |
| FC Echallens | Vaud | Sportplatz 3 Sapins | |
| Grand-Lancy FC | Geneva | Stade de Marignac | |
| FC Martigny-Sports | Valais | Stade d'Octodure | |
| FC Meyrin | Geneva | Stade des Arbères | |
| FC Monthey | Valais | Stade Philippe Pottier | |
| FC Montreux-Sports | Vaud | Stade de Chailly | |
| FC Naters | Valais | Sportanlage Stapfen | |
| FC Renens[2] | Waadt | Zone sportive du Censuy | |
| Signal FC Bernex-Confignon[3] | Geneva | Stade municipal de Bernex | |
| FC Stade Lausanne | Vaud | Centre sportif de Vidy | |
| Vevey Sports | Vaud | Stade de Copet | |
| Club | Canton | Stadium | Capacity |
|---|---|---|---|
| FC Biel-Bienne | Bern | Stadion Gurzelen | |
| FC Bulle | Fribourg | Stade de Bouleyres | |
| SC Bümpliz 78 | Bern | Bodenweid | |
| FC Colombier | Neuchâtel | Stade des Chézards | |
| FC Concordia Basel | Basel-City | Stadion Rankhof | |
| FC Fribourg | Fribourg | Stade Universitaire | |
| FC Grenchen | Solothurn | Stadium Brühl | |
| FC Köniz[4] | Bern | Sportplatz Liebefeld-Hessgut | |
| FC La Chaux-de-Fonds | Neuchâtel | ||
| SV Lyss[5] | Bern | Sportzentrum Grien | |
| FC Münsingen | Bern | Sportanlage Sandreutenen | |
| SV Muttenz | Basel-Country | Sportplatz Margelacker | |
| FC Riehen[6] | Basel-City | Sportplatz Grendelmatte | |
| FC Serrières | Neuchâtel | Pierre-à-Bot | |
| Club | Canton | Stadium | Capacity |
|---|---|---|---|
| FC Altstetten[7] | Zürich | Buchlern | |
| FC Ascona[8] | Ticino | Stadio Comunale Ascona | |
| AC Bellinzona | Ticino | Stadio Comunale Bellinzona | |
| GC Biaschesi | Ticino | Campo Sportivo "Al Vallone" | |
| SC Buochs | Nidwalden | Stadion Seefeld | |
| FC Küsnacht[9] | Zürich | Sportanlage Heslibach | |
| FC Malcantone Agno | Ticino | Cornaredo Stadium | |
| FC Muri[10] | Aargau | Stadion Brühl | |
| FC Red Star Zürich | Zürich | Allmend Brunau | |
| FC Schötz | Lucerne | Sportplatz Wissenhusen | |
| FC Sursee[11] | Lucerne | Stadion Schlottermilch | |
| FC Wangen bei Olten | Solothurn | Sportplatz Chrüzmatt | |
| SC YF Juventus | Zürich | Utogrund | |
| Zug 94 | Zug | Herti Allmend Stadion | |
| Club | Canton | Stadium | Capacity |
|---|---|---|---|
| FC Frauenfeld | Thurgau | Kleine Allmend | |
| FC Freienbach | Schwyz | Chrummen | |
| FC Gossau | St. Gallen | Sportanlage Buechenwald | |
| FC Horgen[12] | Zürich | Waldegg | |
| FC Kreuzlingen | Thurgau | Sportplatz Hafenareal | |
| FC Rapperswil-Jona | St. Gallen | Stadion Grünfeld | |
| FC Rorschach[13] | Schwyz | Sportplatz Kellen | |
| SV Schaffhausen | Schaffhausen | Sportplatz Bühl | |
| FC Tuggen | Schwyz | Linthstrasse | |
| FC Vaduz | Liechtenstein | Rheinpark Stadion | |
| SC Veltheim[14] | Aargau | Sportanlage Flüeli | |
| FC Wetzikon[15] | Zürich | Meierwiesen | |
| FC Widnau[16] | Zürich | Sportanlage Aegeten | |
| FC Winterthur | Zürich | Schützenwiese | |
Winterthur win 4–0 on aggregate and continue to the finals. Vevey Sports win 4–2 on aggregate and continue to the finals. Münsingen win 3–2 on aggregate and continue to the finals. Bellinzona win 5–0 on aggregate and continue to the finals.
Winterthur win 3–1 on aggregate and are promoted to Nationalliga B. Bellinzona win 14–0 on aggregate and are promoted to Nationalliga B.
Montreux-Sports continue to the final. Küsnacht] continue to the final.
Küsnacht win 6–1 on aggregate. Montreux-Sports are relegated to 2. Liga.