Dunedin Railways chief executive Murray Bond said the 60 passengers on the "special trip" were Dunedin Railways staff, contractors and sales agents.
The train stopped at "repair areas", such as where tracks had been reinstated and new culverts had been installed.
The staff had done a "marvellous job" to get the track reopened, Mr Bond said.
It had been closed since July 21.
On Saturday afternoon, about 90 passengers caught the first public train in the gorge, from Dunedin Railway Station to Pukerangi, since the flood.