The party replaced Thein Sein with Vice Chairman U Shwe Mann, China's official Xinhua news agency reports. Shwe Mann also serves as speaker of Myanmar's House of Representatives.
Thein Sein gave up his title as military general and formed the Union Solidarity and Development Party in 2010, starting a series of political reforms that ended military rule.
Shwe Mann, after taking over as party chairman, stressed the need for a multiparty political system in Myanmar.
Myanmar earned praise from the international community for political reforms enacted since 2010. Ongoing violence between Buddhists and members of the minority Muslim community has overshadowed some of those developments, however.
U.N. special envoy on human rights Tomas Ojea Quintana said he had concerns about the outbreak of violence in Myanmar.
"I have received credible allegations that widespread and systematic human rights violations by state officials targeted against the Rohingya (minority) and wider Muslim populations have occurred and are continuing in Rakhine state," he said in a statement.