After a bust up with the Cunninghams (Rovers' owners) at the end of the 1963–64 season, he sensationally quit the Hoops 
He was Bohs' first ever manager as before Thomas Bohs had only ever had coaches or trainers and a Selection Committee of five actually picked the side. It was a homecoming of sorts for Thomas as he grew up on the Phibsborough Road which backed on to Dalymount Park and was an associate member of the club in his early years. Bohs had finished last the previous season and Thomas showed his credentials by managing the then still amateur Bohemians to a 3rd place finish that season, just 5 points behind winners Drumcondra. This was a remarkable achievement considering the rest of the league was professional and Thomas was awarded Irish Soccer Writers' Personality of the Year. The following season, Bohs once again finished 3rd in the league and this time, won the Leinster Senior Cup and Presidents Cup. The performances of his young guns were noticed however and 8 of the amateur team left at the end of the season for the professional ranks; Turlough O'Connor and Jimmy Conway for Fulham and Larry Gilmore and Kevin Murray for Dundalk. He signed a three year contract in April 1966. The predicted collapse never happened and amazingly the "Gypsies" went one better and finished runners-up in the 1966–67 season.
Thomas's abilities didn't go unnoticed and Boston Shamrocks enticed him across the Atlantic for the newly proposed American League. This move turned sour though as Boston failed to gain a place in the elite league and within a year, Thomas had returned to Dalymount Park. After the heroics of the previous seasons, Bohs finished rock bottom of the league without Thomas and were in dire straits financially. 1968/69 brought little joy on the field but off it, an historic EGM of Bohemian members in February 1969 saw the club's constitution changed to allow payment to players. Tony O'Connell, Dinny Lowry and Johnny Fullam were soon signed and in 1970 Bohs won their first major trophy for 34 years when beating Sligo Rovers in the FAI Cup Final. This success meant Bohs would enter European competition for the first time.
During this time Thomas spotted Liam Neeson and he appeared as a substitute against Shamrock Rovers in a trial game.
Bohs finished fourth, third and third again in the next 3 seasons under Thomas's guidance with the young talents of Mick Martin and Gerry Daly flourishing. In July 1973, Thomas sensationally resigned as manager of Bohemians.
He wouldn't be out of the game for long however and later had spells back at Shamrock Rovers, where he won the League Cup in 1976. This triumph was Rovers' first trophy in seven years and it was the 7th different competition Thomas had won with the club.
Sean Thomas had previously managed a League of Ireland XI when they defeated their English counterparts 2–1 at Dalymount Park in 1963. He also managed the Under 23 Republic of Ireland side on three separate occasions - all 0–0 draws with France.