Karunakaran started his school education by joining Vadakara Govt. Lower Primary School in 1923. Later, he studied in Andallur govt. school and the famous Raja's High School near his home in Chirakkal. After passing matriculation from Raja's High School, he went to Thrissur and joined Govt. Fine Arts' college, from where he took degrees in painting and mathematics. For treating an eye disorder, he went to his maternal uncle's home in Vellanikkara near Thrissur, along with his elder brother Kunjirama Marar. Later, he married his maternal uncle's daughter Kalyanikkutty Amma in 1954 at Guruvayoor Temple, when he was 36 and Kalyanikkutty Amma was 30. K. Muraleedharan and Padmaja Venugopal, famous Congress politicians, are their children. It was in 1993, when Karunakaran was the Chief Minister, that Kalyanikkutty Amma died.