Cygan joined Arsenal in July 2002 for £2 million, making his debut in a 1–1 draw with Chelsea on 1 September after coming on as a late substitute for Nwankwo Kanu. While he featured notably in some of the team's more important fixtures, he was mostly considered only a fringe player; he missed the 2003 FA Cup Final through injury, but did pick up a Premier League winners' medal in 2004 after contributing with 18 appearances.