Tens of thousands of commuters may be affected on Wednesday with the T4 Eastern, Illawarra and South Coast lines out of action for several hours.
It means trains from Bondi Junction to Bomaderry won't run on Wednesday, other services may run on a reduced timetable and some stopping patterns could change.
Sydney Trains chief executive Matt Longland said disruptions would likely extend several hours either side of the planned six-hour strike.
"To ensure the safety of our customers, staff, and network overall, trains will need to be taken back to stabling yards and depots before the industrial action starts," he said on Tuesday.
Timetables could be impacted from 6am on Wednesday, but should return to normal by 8pm.
About 70,000 people take the T4 and South Coast line on a normal Wednesday.
"We urge all our customers to plan ahead by catching alternative public transport or working from home on Wednesday, if possible," Mr Longland said.
The Rail, Tram and Bus Union is staging protected industrial action as it seeks to secure changes to a new fleet of intercity trains and reach a new enterprise bargaining agreement.
The new trains have been sitting in storage since 2019 and the previous enterprise agreement expired more than a year ago.
The union has already banned transport officers issuing fines and the industrial action will be escalated to include a strike on Wednesday between 10am and 4pm.
The RTBU said about 90 per cent of train crews would still be available to work, and blamed the government for shutting down the trains.
The union's secretary Alex Claassens said the action had been designed so services could continue.
"There is absolutely no reason for the Illawarra line to be shut down on Wednesday," he said.
"If it is shut down, it will be because Transport bureaucrats have simply decided they don't want to run the trains, not because they can't."
The action was supposed to cause headaches for management and not commuters, he said.
The union has planned area-based strikes three more times before the end of the month, and will also leave station gates open and refuse to operate foreign-built trains on some days.
The union is also banning work associated with the Sydney Metro transit project until September 10.
Transport for NSW says the union action "will progressively degrade service levels across the NSW rail network if they continue as planned".
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