The new series will look at the effects of MDNA on the brain, with Allen and other celebrities being administered the drug.
The study is being undertaken by Imperial College London professors David Nutt and Robin Carhart Harris, reports The Independent.
One celebrity who took part was reportedly turned away after they tested positive for cocaine use.
The documentary - reportedly titled Drugs Live - is scheduled to air in September.
"Keith has a history of drug use and knows very well the highs and lows," a source is quoted as saying in The Sun.
"He's agreed to take part because he thinks Channel 4's show is an important forum for looking at what it means to take drugs - and the effects they have.
"He cannot wait to get stuck in. Who knows what'll happen?"
Channel 4's David Glover said: "This subject is fraught with controversy and confusion. The aim is to bring new clarity to the facts of illegal drug use."
Allen's Princess Diana film Unlawful Killing was recently shelved due to distribution issues.