Derlei signed with FC Porto in the summer of 2002, playing an important part in a successful squad that was also managed by Mourinho. He was one of the top scorers in a side that conquered the UEFA Cup and UEFA Champions League in consecutive seasons – he netted twice in the 2003 UEFA Cup final against Celtic (adding another brace in the 4–1 semi-final win over S.S. Lazio)– being nicknamed "Ninja" while playing for the northern side; the following campaign, as he was leading the domestic goalscoring chart, he suffered a severe knee injury which rendered him unavailable for several months. Derlei was able to come back in time for the UEFA Champions League semi-final against Deportivo La Caruna, where he scored a penalty kick in the second half of the second leg match at the Riazor in Spain which saw FC Porto through to the final 1-0 on aggregate. Derlei would be the starting striker as FC Porto went on to defeat Monaco 3-0 to win the 2003-2004 UEFA Champions League.