The agreement, which will mean the Pompidou sharing some of its 120,000 works of art with the Belgian capital, was signed by Brussels regional government chief Rudi Vervoort and the museum's president Serge Lasvignes this week.
Only 10 percent of the Paris museum's collection is currently on show to the public, despite the opening of branches in the eastern French city of Metz and the Spanish city of Malaga.
The new museum, whose name has yet to be chosen, will occupy about half of a 1930s building currently occupied by a Citroën garage, sharing the 30,000m² premises with an architecture museum and spaces that will be available for performances.
The building's huge windows and art deco design are ideal for an art gallery,
"Citroën and Pompidou are two brands that, culturally, go very well together," Lasvignes commented.
The region bought the garage, the other side of a canal from the Molenbeek district that was home to several of the jihadists involved in November's Paris attacks, for 20.5 million euros and is expected to spend 140 million euros on renovation.
Officials hope the centre will attract 500,000 to one million visitors a year.
National modern art museum closed
Although it has a significant cultural heritage, Brussels is at present better known as the home of European Union bureaucrats than as a cultural tourism destination.
A modern art museum in the city was closed in 2011 due to a controversial decision to turn the premises over to a Fin de Siècle museum that concentrates on the Art Nouveau movement of the 1890s and 1900s.
The federal government's minister responsible for museums, Flemish nationalist Elke Sleurs, has so far refused to hand over the national modern art collection to another level of government and it is unclear whether it will be housed in the new museum, which will be run by the Brussels region.