Eric Flynn was born on 13 December 1939 on Hainan Island, China, where his father was a customs officer for the Hong Kong government. After the outbreak of war and the Japanese invasion of China, his family spent several years interned in a Japanese prisoner of war camp (50 years later he would play a British prisoner in the film Empire of the Sun, set in a Japanese prison of war camp in China).

He returned to Britain at the age of 13, and was educated at Chatham House School in Ramsgate. He then gained a scholarship to Royal Academy of Dramatic Art (RADA), where he met his first wife Fern.

Flynn's sons by his first marriage, Daniel and Jerome, are both actors. He also had a daughter, Kerry, by his first marriage. Flynn married his second wife Caroline, a South African, in 1981. His daughter from his second marriage, Lillie Flynn, finished a three-year acting degree at The Central School of Speech and Drama in 2007 and his son, Johnny, is also an actor and singer