The knockout stage of the 1999–2000 UEFA Champions League began on 4 April 2000 and ended with the final at the Stade de France in Saint-Denis on 24 May 2000. The top two teams from each of the four groups in the second group stage competed in the knockout stage. For the quarter-finals, each group winner was randomly drawn against the runner-up from another group, with the group winner hosting the second leg. The four quarter-final winners were then drawn together for the semi-finals, the winners of which contested the final.

Each quarter-final and semi-final was played over two legs, with each team playing one leg at home; the team that scored the most goals over the two legs qualified for the following round. If the two teams scored the same number of goals over the two legs, the team that scored more goals away from home qualified for the next round; if both teams scored the same number of away goals, matches would go to golden goal extra time and then penalties if the teams could not be separated after extra time.