Thomas's vlei rat (Otomys thomasi) is a species of rodent in the family Muridae. It is endemic to Kenya's high plateau mountains of the Rift Valley.
Osgood (1910) initially described this species as Otomys thomasi. In 2006, it would be included under Otomys orestes (afroalpine vlei rat) by Carleton & Byrne. Taylor et al. (2011) reviewed the genus Otomys and moved Otomys thomasi back to species status.
It is known from less than 10 locations in Kenya and isn't recorded in protected areas, hence the assessment of the species as "Vulnerable" by the IUCN.