In 1988, Chapman appeared in the Iron Maiden video "Can I Play with Madness". The same year, he starred in a pilot of a proposed television series, Jake's Journey, but financial problems prevented a full series from being made. In 1988, he also appeared on stage with three other Pythons (Gilliam, Jones and Palin) at the 41st British Academy Film Awards where Monty Python received the BAFTA Award for Outstanding British Contribution To Cinema.
In 1988, Chapman made a routine visit to a dentist, who found a small, malignant tumour on one of his tonsils, leading to both being removed via a tonsillectomy. The following year, the cancer had spread into Chapman's spinal cord, where another tumour was surgically removed. Chapman had several chemotherapy treatments and surgeries during the final months of his life, but ultimately the cancer was declared inoperable. According to his brother, Chapman was visibly upset by the death of his mother that July, by which time he was terminally ill. Shortly afterwards, Chapman filmed scenes for the 20th anniversary of the first broadcast of Monty Python’s Flying Circus, the final time he appeared on television.