It was revealed in January that the Rooneys had told their team of handlers to stop entering their horses at the track as they believed their runners were at further risk of injury at the Cotswold venue.
However, following regular communication with the course their self-imposed exile has come to and end.
A statement issued on behalf of the owners said: "As was widely reported in the media at the time, at the end of last year Paul and Clare Rooney instructed their trainers to suspend making their entries for races at Cheltenham Racecourse. That instruction was given in light of concerns over injury rates at the course.
"Since then, Paul and Clare Rooney have been in regular communication with the racecourse and with the BHA. Extensive information and data about all aspects of horse welfare at the course has been made available to them. They have also undertaken their own investigations into such matters.
"Those communications culminated in a meeting last week between Simon Claisse, Regional Head of Racing and clerk of the course at Cheltenham, and Jason Maguire, racing manager to Paul and Clare Rooney.
"In light of such matters, Paul and Clare Rooney have confirmed that they have instructed their trainers that they may resume making entries for races at Cheltenham. They look forward to supporting the course in future as part of their overall commitment to National Hunt racing."
Ian Renton, Cheltenham and South West Regional Director at Jockey Club Racecourses, added: "We are pleased that Paul and Clare have decided to make entries at Cheltenham and look forward to their horses competing at the Festival.
"The team here takes immense care to provide a safe, world-class racing surface for more than 1,500 racehorses each year. The BHA inspects the course on a regular basis to ensure the highest welfare standards are delivered and that is a priority that has our total commitment."
