In March 1962, Ayub Khan suspended the Martial Law and proclaimed the Constitution of 1962. Presidential elections were held in January 1965, and Ayub Khan defeated Miss Fatima Jinnah, Jinnah's sister, to once again become the President of Pakistan.

During his term, the "Great Decade" was celebrated, which highlighted the development plans executed during ten years of Ayub's rule. The 1965 War was fought during Ayub's term and Ayub Khan represented Pakistan in the subsequent Tashkent Talks.

Ayub Khan moved the capital of Pakistan from Karachi to Islamabad in 1965, but could not complete his term due to public pressure.

He handed over power to General Muhammad Yahya Khan on March 25, 1969.