The 25-year-old, who was diagnosed with nodular sclerosing Hodgkin lymphoma in October, announced on Twitter that he was in "complete remission".
Thompson has undergone a six-month course of chemotherapy.
The former Rochdale midfielder, who has spent the past two seasons at Tranmere, is now targeting a quick return to first-team football.
Speaking to BBC Late Kick Off in March, Thompson revealed he had received support from other sporting cancer survivors following his diagnosis, which was made after he complained of increased fatigue and illness.
Among them was tennis player Ross Hutchins, who successfully beat Hodgkin lymphoma in 2013.
While undergoing treatment, Thompson has raised more than £16,000 for Leukaemia & Lymphoma Research as part of the "Grow 4 Joe" campaign, with team-mates and footballers from other clubs pledging to grow their hair in the closing weeks of last season.
Tranmere Rovers winger Joe Thompson has been given the all-clear by doctors following a battle with cancer.