Services are operated to Bendigo and Echuca primarily using V/Line VLocity diesel multiple unit sets in either 3- or 6-car configurations; V/Line N class loco-hauled services run to Swan Hill, with a mixture of N type carriages and Z type carriages.

[3] As part of the Regional Fast Rail project, which was completed in 2006, the Bendigo line underwent major track upgrades that would allow for V/Line VLocity diesel multiple unit trains to be introduced to the line, running at speeds of up to 160km/h between Sunbury and Bendigo.

Controversially, between Kyneton and Bendigo the line was singled, officially to allow for better clearance past heritage structures, although some double-track sections were retained, effectively creating long crossing loops.

While the project was overall well-received for increasing service reliability, the choice to bypass North Melbourne was especially criticised.

[9] The advent of the Bendigo Metro Rail Project has significantly increased the frequency of trains to Epsom, Eaglehawk, and Kangaroo Flat.

[10] The Regional Rail Revival project primarily focused on upgrades to the Echuca and Swan Hill services.

[15] Trains operate approximately once an hour between Southern Cross and Bendigo every day, with some services originating or terminating at Epsom or Eaglehawk.