Burundian President Pierre Nkurunziza. (Jean Pierre Harerimana/Reuters)

BURUNDI IS facing the worst crisis since its bloody civil war.

In 1993, the landlocked country of 10 million was devastated by massive ethnic violence between Hutus and Tutsis, sparked by the assassination by Tutsi military officers of Melchior Ndadaye, the first democratically elected and first Hutu head of state. Some 300,000 people were killed during years of conflict.

In 2000, the Arusha Peace and Reconciliation Agreement, backed by the United Nations, provided a framework to end the violence. The agreement aimed to ensure power-sharing among ethnic groups. It mandated that a president serve no more than two terms in office.

In direct violation of the Arusha treaty, President Pierre Nkurunziza, who came to power in 2005, registered Friday to run for a third term in office in elections scheduled for June 26. A constitutional court conveniently ruled that Mr. Nkurunziza’s first term in office did not count, as he was picked by lawmakers, not elected. Fears of violence have sent 50,000 Burundians fleeing the country, with more than half seeking refuge in neighboring Rwanda. Protests have erupted in the capital of Bujumbura, with at least 13 killed and more than 250 arrested. The opposition has promised to continue protesting until Mr. Nkurunziza steps down. His spokesman has retorted that the government will “stamp out” the protests.

The political crisis could devolve into a tragic reprise of ethnic conflict between Burundi’s Hutu majority and Tutsi minority. The turmoil also has consequences for other nations in the Great Lakes Region. The 25,000 refugees fleeing to neighboring Rwanda, which suffered its own Hutu-Tutsi slaughter, could trigger old ethnic tensions there. Tanzania has warned of a humanitarian crisis, with as many as 17,000 Burundian refugees reportedly crossing into the country in the past several weeks. Nearly 8,000 more Burundians have fled into the South Kivu province of Congo, a country not known for stability.

To defuse the situation, Mr. Nkurunziza should set aside his candidacy and stop cracking down on journalists, radio stations, social media sites and other elements of civil society. Mr. Nkurunziza’s actions are a bad model in a fragile neighborhood. There are fears that Paul Kagame, who has ruled Rwanda since the end of its 1994 genocide, may rewrite his country’s constitution to seek an additional term in 2017. President Joseph Kabila of Congo is nearing the end of his two-term limit but has given no guarantees that he will step down.

Secretary of State John F. Kerry said this week that Mr.­­ Nkurunziza’s actions fly “directly in the face of the constitution.” The African Union called for the postponement of the June elections. Ideally, the union and the East African Community, a regional intergovernmental organization, should use their regional leverage more strongly. But with neighbors such as Rwanda and Congo, such an outcome seems unlikely, which is tragic for Burundians.