Thomson replaces Derek Pereira, who was at the helm since 2013 and guided them to a eighth-place finish in last season's league.
Thomson has previously gained coaching experience at British clubs Celtic, Rangers, Blackpool FC, Birmingham City, Limerick, Dundee United and Inverness and Dubai-based club Al Ahli.
"I am looking to build on the great work that Salgaocar FC has done in the past. I am looking forward to coming over soon and adding value to the coaches, players and staff at the club. I have read and been told that Salgaocar FC is one of the most professional teams in India with a long history." the 48-year-old said in statement.
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