Šuker joined FA Premier League club Arsenal for the 1999–2000 season. He made his league debut on 22 August 1999 in a 2–1 defeat to Manchester United at Highbury, coming on as a substitute for the final 15 minutes. He played another two matches as a substitute before making his first start in Arsenal's 3–1 home victory over Aston Villa, where he scored a brace, his first two goals in the Premier League. With Arsenal, he played in the 2000 UEFA Cup Final as an extra-time substitute, Šuker missed his penalty as Arsenal lost to Turkish side Galatasaray on penalties.