The union representing rail staff had warned weeks ago that this morning was likely to be a particularly challenging day, as too many staff had been granted leave.
Sydney Trains has announced almost 40 services will be cancelled in the morning and evening peaks.
In addition, the Hornsby Junction will reopen, which could cause delays as drivers adjust to the remodeling.
The disruptions follow last week's (Jan 9) troubles where scores of trains were cancelled or delayed on most lines.
