Petra De Sutter of the Flemish Green party, Groen, was announced as one of the country's Deputy Prime Ministers, according to a statement by the European Greens on Thursday.
De Sutter, who has been a member of the European Parliament since July 2019, was appointed to the post alongside six other politicians, the Reuters news agency reported.
Belgium had not had a full-fledged government since December 2018, when a four-party collation collapsed.
Between the 2019 federal elections and March this year, it was governed by a caretaker administration led by the country's first female Prime Minister, Sophie Wilmes, who is now the country's first female Foreign Minister.
De Sutter is a professor of gynecology, specializing in fertility, at the University of Ghent. She is a vocal advocate for trans rights and reproductive rights, and has spoken openly about her own experiences of being a trans woman.
"I was forty when I decided to fully become the woman that I always were and because of this decision I lost colleagues, people I knew and even friends," she said in an interview published to her website.
"Not everybody has had the luck in life that I had, in being accepted in my working environment, being accepted by my partner and love. In fact, very few people in my situation had this luck," she said.
"This is why I need to do something, for those who lacked this luck. I have a very strong feel of justice and find it so unjust that people in the world suffer simply because of who they want to be," she added.
De Sutter welcomed her appointment on Twitter, writing: "Incredibly grateful for the trust I have received from my party. Last night, alongside 1,000 other members, I gave the green light for the new government."
"Now, with that government, I can do what is necessary to relaunch our country and work on a new future for all Belgians," she added.
De Sutter is now Europe's most senior transgender politician. Marie Cau became France's first transgender politician when she was elected Mayor of Tilloy-lez-Marchiennes earlier this year, and Italy's first transgender politician Gianmarco Negri took office as mayor of Tromello last year.