Clinton was due to visit the capital, Abuja, this week, along with Baroness Patricia Scotland, Secretary General of the Commonwealth.
The planned trip was facilitated by the Kofi Annan Foundation and the National Peace Committee (NPC).
Clinton spokesman Angel Ureña said in a statement that Clinton will not visit Abuja.
The statement said Clinton would continue to support the AFN's work for peaceful and fair elections in Nigeria.
He was about to deliver a keynote address at a peace signing ceremony by the presidential candidates.
Clinton will speak later this week with re-election candidate Muhammadu Buhari and his main opponent Atiku Abubakar, his spokesman said.
More than 200 people were killed and about 40,000 people displaced in violence after the presidential elections in Nigeria in 2011, when then-elected Goodluck Jonathan defeated Buhari in the elections.
