Glaetzer finished third in the men's Keirin in Cambridge, trailing only Russia's Shane Perkins and Malaysian triumphant Azizulhasni Awang.
The podium finish carries added significance for the 27-year-old, who was diagnosed with thyroid cancer in October and has since had surgery to remove a tumour in his throat.
Having helped his nation to six medals in New Zealand, Glaetzer will now return to Australia to contest the next round of the World Cup, before resuming his radiotherapy treatment.
Glaetzer is a two-time track world champion and three-time Commonwealth gold medallist, and while it is believed cancer fatigue has affected his performance, he remains on track to compete at the 2020 Tokyo Olympics.
"One of the first thoughts I had in regard to my cycling career and Tokyo was 'I'm not going to let this stop me', if I am able to and if it's safe to, then you know what? I'm not going to let this have power over what I do," Glaetzer said.
"I have some goals I want to achieve and Tokyo is the big target, that hasn't changed. I'm not going to stop chasing the Olympics and being the best in the world."