V/LINE train services will be back up and running across the entire transport system from Monday.
Trains will operate as timetabled from Bendigo and Swan Hill to Southern Cross Station.
Services were disrupted for two weeks after more than 300 V/Line staff had to isolate and get tested for COVID-19.
Read other news: Bendigo police investigate Kangaroo Flat pursuit
Coaches will continue to replace Echuca line trains between Echuca and Bendigo until October 31 due to upgrade works.
"We apologise to passengers who were making permitted journeys over the last two weeks for the disruption to their journey," a department of transport spokesperson said.
"We thank them for their continued patience and understanding while we worked to return train services across the network as quickly and safely as possible."
Our journalists work hard to provide local, up-to-date news to the community. This is how you can access our trusted content:
Sign up for our newsletter to stay up to date.