The Have I Got News For You panellist will front an edition of the show next week, following the imminent departure of Adrian Chiles.
Also stepping in will be Watchdog host Matthew Allwright, who will host the majority of editions in the next fortnight.
Chiles dramatically announced he was quitting The One Show last week after signing a deal with ITV which sees him heading to the GMTV sofa and a range of other programmes including football coverage. His final programme is on Friday.
Allwright will be unable to present on Thursdays because of his Watchdog duties and Merton will anchor the show on May 6. The Thursday edition for the following week has not yet been filled.
Chiles became disenchanted when it emerged that Radio 2 breakfast show host Chris Evans was being brought in to present The One Show on Friday evenings.