Ndadaye's assassination during a coup attempt in October after three months in power provoked the Burundian Civil War between Tutsis and Hutus.

[1][5] In 1988, President Pierre Buyoya decreed the creation of a 24-person commission to study ethnic divisions in Burundi and create a plan for national unity.

[6] Ntibantunganya served on the panel, which produced a Charter of National Unity, but it was denounced by Hutu members of the political opposition for being dominated by Tutsis and presenting an elitist point of view of the country.

[12] Early in the morning on 21 October 1993 Tutsi soldiers in the Burundian Army launched a coup and attacked the presidential palace.

[10] Thus informed, he began calling FRODEBU leaders in an attempt to rally the government and warned Minister of Communications Jean‐Marie Ngendahayo.

Distrustful of his military guard, Ntibantunganya changed into his gardener's clothes and walked to a friend's home, where he remained in hiding for the next two days.

By his own account, Ntibantunganya decided to withdraw himself as a candidate[19] despite having the support of the central committee,[21] citing his desire to focus on party matters, and Ngendahayo suggested that FRODEBU back Cyprien Ntaryamira for the position instead.

[22] Following the crash, Ntibantunganya made a broadcast on Burundi television, flanked by the minister of defence and the army chief of staff, appealing for calm.

Prime Minister Anatole Kanyenkiko and his government officially resigned but stayed in power pending the confirmation of a new executive.

Faced with the spillover of the Rwandan Civil War, Ntibantunganya's government pursued a strict policy of neutrality, denying officials of the former Habyarimana regime residency in Bujumbura and refusing to allow French troops to use Burundi as a staging area for Opération Turquoise.

Moderates in both UPRONA and FRODEBU were marginalised as radicals gained increasing influence and ethnic violence permeated the countryside.

[28] By the middle of the year Ntibantunganya was the only original member of the FRODEBU central committee still actively engaged with the party and the civil political process, with the others having been killed or having fled into exile.

[11] The party fractured into at least three groups, with the smallest section supporting Ntibantunganya, though many felt his cooperation with and concessions to the army and the opposition amounted to a capitulation.

At the behest of Tutsi extremists he also convinced the National Assembly to grant the army and gendarmerie emergency powers to restrict freedom of movement and speech.

[31] With the civil war worsening and ethnic violence increasing, on 25 June 1996 Ntibantunganya participated in regional security talks in Mwanza, Tanzania.

When Ntibantunganya attempted to attend a funeral for them three days later[32] the crowd of mourners attacked him with stones, forcing him to evacuate via helicopter.

He announced the suspension of the constitution, the dissolution of the National Assembly, and the banning of political parties, but declared that he would guarantee Ntibantunganya's safety.

He left the United States Embassy on 8 June 1997, saying, "I reaffirm that I shall not yield on the principle for a search for a negotiated solution for all problems that face our country.

[37] In July he and several other opposition candidates dropped out of the race, citing concerns for their safety and fear that incumbent President Pierre Nkurunziza would rig the outcome in his favor.

[1] During the celebration of International book day on 23 April 2021 he lamented that Burundians "do not read" and called for the national promotion of literature.