Goodall was born in 1822, the second son of steel line engraver Edward Goodall (1795–1870). He received his education at the Wellington Road Academy. Frederick's first commission, for Isambard Brunel, was six watercolour paintings of the Rotherhithe Tunnel. Four of these were exhibited at the Royal Academy when Frederick was 16. His first oil won a Society of Arts silver medal. He exhibited work at the Royal Academy 27 times between 1838 and 1859. He was elected Associate of the Royal Academy in 1852.
Goodall visited Egypt in 1858 and again in 1870, both times travelling and camping with Bedouin tribesmen. In order to provide authentic detail to his paintings, Goodall brought back sheep and goats from Egypt. The Eyptian theme was prominent in his work, with 170 paintings being exhibited at the Royal Academy over 46 years. Goodall's work received high praise and acclaim from critics and artists alike and he earned a fortune from his paintings. He had a home built at Grim's Dyke, Harrow Weald, where he would entertain elaborate guests such as the Prince of Wales (later Edward VII).