S.A. Ajayi returned to Kabba Province and joined the Northern People's Congress, where he later rose to become the vice president of the party in Kabba Province. In 1955, he was elected councillor in the Kabba Native Administration and a year later, he won a seat in the Northern House of Assembly, and became a member of the regional executive council as minister of state for forestry affairs. He was appointed acting minister for education in 1963, in the absence of Isa Kaita. During his time in the Northern House of Assembly, he was appointed parliamentary secretary to the Premier of Northern Nigeria, Ahmadu Bello from 1957 to 1960. He was among the delegate that negotiated Nigerian Independence at the Lancaster House Conferences in London and led the Northern Nigeria Delegation to London for the Negotiation and Launching of VC-10 Nigeria Airways. He was a member of Nigeria Economic Mission to West Germany and was a minister till their government was overthrown by the military coup on January 15, 1966. During Shehu Shagari's administration, he was appointed to the first board of directors of National Insurance Corporation of Nigeria (NICON).