Thomas was heading to Melbourne for a global AIDS conference along with dozens of others on the MH17 flight that ended in tragedy on Thursday.
"It is with deep sadness that WHO lost one of our colleagues in the Malaysia crash," communications official Gregory Hartl told reporters in Geneva.
Thomas came to WHO from the BBC and was passionate about public health issues, Hartl said, flanked by press service colleagues, several in tears.
"His twin sister said he died doing what he loves," Hartl said, adding that no other UN staff were aboard the doomed airliner.
Many of the journalists attending the briefing had worked with Thomas, and a minute of silence was held in his memory.
The Boeing 777 was on its way to Kuala Lumpur from Amsterdam when it crashed near the village of Grabovo close to the border with Russia, amid fears it was shot down.
There were no survivors.