Kotoka was born on 26 September 1926 in Alakple, a village in the Keta district of the Volta Region. He attended the Alakple Roman Catholic School and later the Anloga Senior School.

He enlisted in the infantry school of the Gold Coast Regiment in 1947 and rose through the ranks. Kotoka was commissioned as a lieutenant in 1954 after training at Eaton Hall Officer Cadet School in the UK.

In 1960, Kotoka led Ghana's contingent in the UN Operation in the Congo, earning him the Ghana Service Order for Exceptional Bravery in 1963.

Kotoka played a crucial role in the military coup that overthrew President Kwame Nkrumah on 24 February 1966. He announced the coup to the nation and became a member of the National Liberation Council.

On the day of the coup, Kotoka was promoted to Major General and later to Lieutenant General on the first anniversary of the coup. He served as General Officer Commanding the Ghana Armed Forces and Commissioner for the Ministry of Health.

Kotoka was assassinated on 17 April 1967 during an attempted coup known as "Operation Guitar Boy." He was killed by Lt. Moses Yeboah and his men.

The Kotoka International Airport in Accra was named in his honour.