The first passenger flight took off from the airport in Brussels where suicide bombers carried out a deadly attack nearly two weeks ago.
The blasts there and at a nearby metro station killed 32 people and destroyed the airport's departure area.
A Brussels Airlines plane heading to the Portuguese city of Faro was the first of three flights scheduled to leave the airport Sunday evening. The airport is calling them "symbolic flights" with more to be added in the coming days.
"A restart of the operations, even only partially, as quick as this is a sign of hope that shows our shared will, and our strength to resurface and not to let our heads down," Brussels Airport Company CEO Arnaud Feist said Saturday.
Feist also announced temporary repair work and security features that will be used at the airport as it works toward a return to full operation, which will take months.
Passengers check in at Brussels Airport, which partially re-opened following a bomb blast 12 days ago, in Zaventem, Belgium, April 3, 2016.
Belgian police complained about what they said had been lax security at the airport and threatened to strike unless certain measures were taken, but have reached an agreement with the government.
Police also made several arrests Saturday following a tense confrontation between right-wing protesters and anti-racist youth in Brussels.
A far-right group had planned a demonstration in Molenbeek, a predominantly Muslim neighborhood where a number of the November 2015 Paris attackers were based.
An anti-racist group had called for a counterdemonstration.
Both groups were banned by local authorities, fearing a repeat of last Sunday's disturbance, when police fired water cannons to break up about 450 protesters.
Belgian television showed some 30 far-right marchers in a suburb of Brussels, holding a banner reading: "This is our country."