In 2009 Boyle was censured by the BBC Trust for comments about Olympic swimmer Rebecca Adlington, following her gold-winning success at Beijing the previous year.
His remarks, made during an edition of the Mock The Week TV programme, were ruled to be offensive but no further action was taken, which prompted her agent to complain about the "slap on the wrist" when Adlington had been humiliated.
Channel 4, which previously broadcast several of Boyle's shows including Tramadol Nights and The Boyle Variety Performance, distanced itself from the comic.
A spokesman for the Paralympics broadcaster said: "Frankie Boyle was tweeting from his personal account and not on behalf of Channel 4. He is not under contract and there are no shows planned with him."