The as-yet-unnamed player was sold by his club in a multi-million pound deal, but his new team were not informed of the positive drug test, the programme claims.
However, the star will be exposed tonight during a Dispatches special on the use of recreational and performance-enhancing drugs in football.
The flagship Channel 4 investigation series claims to have uncovered the identities of dozens of footballers who have tested positive for cocaine and cannabis. It says that their names were kept secret by the Football Association and their clubs.
Dispatches, which is now working more closely with Channel 4 News presenter Jon Snow, also said that 240 drug tests had been abandoned between April 2007 and August 2010, after the players were absent when officials turned up at their training grounds.
The FA said that it abides by the World Anti Doping Agency (WADA) code, but the agency's David Howman called on the body to be more open about testing.
"If you don't [be more transparent], then you are susceptible to an allegation you're hiding something," he told reporters.
"They're saying they haven't got a doping problem because there are not many positive tests. I think the answer to that is: don't we need to conduct better research to see what the prevalence of doping is?
"Until we are satisfied by the use of all the gathering of evidence I don't think we're in a position to say [that there is not a drug problem in English football]."
In a statement to Dispatches, the FA said: "The FA operates a comprehensive anti-doping programme which is the largest of any sport in the UK.
"The FA go beyond the WADA Code by proactively testing all samples for social drugs, irrespective of whether the tests are conducted in or out of competition."
Dispatches: The Truth About Drugs In Football airs tonight at 8pm on Channel 4.
In February, West Yorkshire police arrested a man on charges of alleged assault after viewing undercover footage shot by Dispatches in a mosque at Keighley.