Following political transition in 1985, Turabi reorganised the former party into the National Islamic Front (NIF), which pushed for an Islamist constitution.

The NCP was established in 1998 by key political figures in the National Islamic Front (NIF) as well as other politicians.

As the sole political party in the state, its members quickly came to dominate the entire Sudanese parliament.

Reportedly, al-Turabi was suspended as Chairman of National Congress Party after he urged a boycott of the President's re-election campaign.

Then, a splinter-faction led by al-Turabi, the Popular National Congress Party (PNC) which was renamed the Popular Congress Party (PCP) shortly afterwards, signed an agreement with Sudan People's Liberation Army (SPLA), one of the largest rebel groups in the country, which led al-Bashir to believe that they were plotting to overthrow him and the government.

[10] In 2000, following the Sudanese government approving democratic elections that were boycotted by the opposition, it merged with the Alliance of Working Peoples' Forces Party of former President Gaafar Nimeiry.

Since the outbreak of the War in Darfur in 2004 between the government of Omar al-Bashir and rebel groups such as the Sudanese Liberation Army (SLA) and the Justice and Equality Movement (JEM), the NCP has been almost universally criticised for allegedly, however not officially, supporting Arab militias such as the Janjaweed through a campaign of murder, rape and deportation against the militants as well as the local population.