Juan Carlos Bernegger (born 9 March 1969) is an Argentine-Swiss football manager and a former player who played as a midfielder. He is the current assistant manager of FC Zürich.
Bernegger had a brief career in football with Belgrano in Argentina and then Winterthur in Switzerland, but had to retire because of ligament injuries in 1993 at the age of 21. Bernegger decided to stay in Switzerland, and made his name as a youth scout and youth coach for Winterthur. Bernegger became long-term youth coach for Grasshopper, and after a couple stints at Basel U21 and Luzern rejoined Grasshopper as the head manager in 2016.
From 2018 until 2020, he worked as assistant under Marcel Koller at FC Basel and won the won the Swiss Cup in 2019.
On 4 May 2022, FC Thun announced that Bernegger will leave the club at the end of the 2021âÂÂ22 season.
In August 2023, he rejoined Koller as his assistant at Egyptian giants Al Ahly SC. He departed Al Ahly when Koller was sacked in April 2025.
On 2 March 2026, he joined FC Zürich as assistant manager to head coach Dennis Hediger.
Bernegger's grandparents emigrated from St. Gallen, Switzerland to Argentina after World War II.