The qualifying round of the 1999–2000 Nationalliga A season was contested by twelve teams. The first eight teams of the First Stage (or Qualification) were then to compete in the Championship Round. The season started on 7 July. Basel's priority aim was to reach the Championship stage and end the season in the top three. The season started sub-optimal, the team remained unbeaten, but with just three wins and four draws in the first seven rounds, they lost contact to the table leaders. Following their first defeat, in the away game against Lausanne-Sport, Basel improved their position in the table with another three victories. Basel suffered their first home defeat on 2 October against Yverdon-Sports, but they ended the Qualification Round in second position in the league table. The Championship Round started on 12 March 2000. The participating teams took half of the points (rounded up to complete units) gained in the Qualification as bonus with them. Basel played amongst the table leaders and in the tenth round they even managed a 3–1 victory against league leaders St. Gallen. However, in their last four matches Basel won only two further points and dropped to third position behind champions St Gallen and Lausanne, against whom the final game of the season ended in a 0–3 home defeat on 7 June 2000. Nevertheless, Basel qualified for the 2000–01 UEFA Cup.
