Sydney's Monday morning commute was back on track thanks to 400 engineers who worked through the night to fix a problem caused by a scheduled upgrade to the train networks signalling system.

Trains were cancelled and thousands were left stranded on Sunday after the replacement of a 39-year-old signal box with a new digital system.

Passengers took to social media to vent their frustration at being left to wait for hours as officials tried to compensate with replacement buses and rerouted trains.

Chief executive of Sydney Trains, Howard Collins said that the system update was one of the most complex pieces of engineering work to be undertaken on the rail network.

Collins said that while people would not be reimbursed for their train fare, Sydney Trains would consider compensating people if they had missed flights because of the delays.