Diplomatic relations between Malaysia and Nigeria were established in 1965, soon after Nigeria achieved its independence in 1960. Malaysia's Mission in Lagos, which was established in 1965, was its first resident Mission in the Sub-Sahara region.
Malaysia's first High Commissioner to Nigeria was YTM Tuanku Jaafar ibni Almarhum Tuanku Abdul Rahman from 1965 to 1967.
The High Commission of Malaysia was later relocated to Abuja, the Federal Capital Territory in August 2006. Nigeria established its Mission in Kuala Lumpur in 1991.