The 1998–99 Campionato Sammarinese di Calcio season was the 14th season since its establishment. It was contested by 16 teams, and S.C. Faetano won the championship.
Regular season
Group A
Group B
Results All teams play twice against the teams within their own group and once against the teams from the other group.
Championship playoffs
First round F.C. Domagnano 1–0 S.C. Faetano S.P. Tre Penne 1–3 S.S. Cosmos
Second round S.S. Folgore/Falciano 2–1 S.S. Cosmos S.S. Murata 2–3 F.C. Domagnano
Third round S.S. Murata 2–3 S.P. Tre Penne S.S. Cosmos 1–2 S.C. Faetano
Fourth round F.C. Domagnano 3–3 (pen 6–7) S.S. Folgore/Falciano S.P. Tre Penne 1–2 S.C. Faetano
Semifinals F.C. Domagnano 1–1 (pen 1–4) S.C. Faetano
Final S.C. Faetano 1–0 S.S. Folgore/Falciano
References San Marino – List of final tables (RSSSF)