Htin Kyaw from the National League for Democracy (NLD) takes over from Thein Sein, who introduced wide-ranging reforms during his five years in power.
Although NLD leader Aung San Suu Kyi is barred from the presidency, she has said she will rule by proxy.
The handover completes the transition that began after the NLD won a landslide win in elections in November.
Thein Sein became president of a quasi-civilian government in 2011 - ending decades of military rule -and is credited with starting the reform process in Myanmar, also known as Burma.
Htin Kyaw won the presidential vote in parliament earlier this month, beating another candidate from the NLD and a military-nominated candidate with 360 of the 652 votes cast.