Julian Weigl was formed at TSV 1860 Munich, debuting in the 2. Bundesliga in February 2014 and becoming the youngest captain in the club's history at 18. He joined Borussia Dortmund in 2015 and made more than 150 appearances as a deep-lying midfielder, scoring his first professional goal against Sporting CP in the Champions League.

Benfica signed him on 2 January 2020 for a reported 20 million euros on a contract to June 2024. He became a fixture in midfield across two and a half seasons, appearing in more than 100 matches and captaining the side on occasion.

Weigl started 2022/23 under Roger Schmidt but, with Enzo Fernández, Florentino Luís and Chiquinho competing for places, he was allowed to leave on 1 September 2022 on loan to Borussia Mönchengladbach. The German club exercised a buyout clause of around seven million euros on 5 May 2023, signing him permanently on a five-year deal, so his Benfica career ended with the club on its way to the 2022/23 Primeira Liga title. He moved to Al-Qadsiah in September 2025.