As a boy, Gruffydd was one of the hostages taken by King John as a pledge for his father's good faith. On his father's death in 1240 he would under Welsh law have been entitled to consideration as his father's successor. Llywelyn however had excluded him from the succession on the grounds of his illegitimacy and had declared his only legitimate son by his wife Joan, Dafydd, to be his sole heir. Llywelyn went to considerable lengths to strengthen Dafydd's position, probably aware that there would be considerable support for Gruffydd against the half-English Dafydd.
Gruffydd was held a prisoner by his brother Dafydd when the latter took over Gwynedd. Following a successful invasion of the Welsh borders by King Henry III of England in 1241, Dafydd was obliged to hand over Gruffydd into the king's custody whence he was taken to London and imprisoned in the Tower of London. Gruffydd's wife, Senana (who was daughter of Caradoc ap Thomas of Anglesey, a member of their dynasty), agreed to pay Henry 600 marks for the release of her husband and their eldest son, Owain, and to hand over her two youngest sons, Dafydd and Rhodri, to the king as hostages to ensure that she kept her part of the bargain. Henry did not keep his part however, and kept Gruffydd and his son imprisoned as "guests" because this continued to give him the possibility of using Gruffydd as a weapon against his brother. However, the headstrong and impatient Gruffydd died while attempting to escape from the Tower in 1244. He is said to have used an improvised rope made from sheets and cloths to lower himself from his window, but as he was a heavy man the rope broke and he fell to his death. His body was discovered by the Yeoman of the Guard the next morning at the foot of the White Tower where he had fallen some ninety feet to his death. The window from which he made his descent is on the south side of the White Tower on the top floor. It was bricked up afterwards and can still be seen today. In 1248 the abbotts of Strata Florida and Aberconwy arranged for the return of his body to Wales where he was buried at Aberconwy with his father.