The first trains stopped turning around 9:00 pm (2000 GMT), travellers said on Twitter.
High-speed international Eurostar, Thalys and inter-city Belgian trains had warned passengers in advance it would be Tuesday mid-day before the network was functioning normally again.
Southern Charleroi airport -- a key low-cost hub -- was expected to be out of action Monday, but the main international runways at Brussels were due to be functional.
The Belgian government arranged fallback emergency access via a military airport for European Union leaders who needed private landings.
Staff working in the summit venue in uptown Brussels were warned they might have to appear before 5:30 am -- for a 1400 GMT gathering -- to escape picket lines.