The 6ft 6in lock, who was born in Edinburgh, returns to the Capital from Sydney-based Warringah Rugby Club - whom Scotland head coach Gregor Townsend represented in the early 1990s - where he has spent the last three years.
He will link up with his new team-mates ahead of the Guinness PRO14 campaign.
Thomson said of his homecoming: “I’m really excited to be joining Edinburgh. I’ve been in Australia for three seasons now and loved my time out here, but the opportunity to come home and play in a professional environment is exactly what I’ve been working for.
“I’m looking forward to challenging myself in the PRO14 and contributing towards the success of the club this coming season."
Head Coach Richard Cockerill welcomed the arrival of the 25-year-old, adding: “We’re delighted to have secured the signing of Sam. He is a lock who possess both size and skill and we’re excited to see how that skillset develops further within our pack.
“Sam has played a fast-paced style of rugby in both the Shute Shield and NRC in Australia, so we hope that match experience will translate into the type of game we’re trying develop here at Edinburgh.
“We’ve obviously lost a large number of our pack to the World Cup, so we’re keen to see Sam hit the ground running and make an impact from the get-go.”
Thomson attended Kelvinside Academy and played for Glasgow District at Under-15, Under-16 and Under-17 level. He attended the University of Worcester while playing for Lydney RFC, and represented the Scottish Exiles Under-18s, before a six-month spell with New Zealand side Southbridge Rugby, where Dan Carter began his career.
He joined Perpignan's academy ahead of the 2015/16 season but returned to Scotland the following year, enrolling as a Stage 3 player with the Fosroc Scottish Rugby Academy while being affiliated to Glasgow Warriors.
He debuted for the Scotstoun side against Ulster in September 2016 but suffered a season-ending shoulder injury and returned to the Southern Hemisphere with Warringah, playing a key role as the Rats won the Shute Shield in 2017 with a 30-25 win over Northern Suburbs in the final.
Thomson, who led the league in lineout wins and steals in consecutive seasons, competed in the National Rugby Championship for the Greater Sydney Rams, NSW Country and Sydney while continuing to feature for Warringah in his second and third terms in Australia.
He is also a qualified canoe/kayak instructor and has passed mountain leader training.