Wilkinson, was a presenter of Milkshake!, the early-morning programming block for young children on Channel 5 and Finger Tips for CITV. Wilkinson took over as the host from Fearne Cotton in series two and remained as the host until the series closed. Prior to joining Milkshake! in 2000, Wilkinson co-presented the breakfast show Wakey! Wakey! for the now-defunct children's channel Carlton Kids. As well as presenting for Milkshake, she has also starred in Milkshake shows such as Havakazoo and Monkey Makes. Naomi Left Milkshake in 2010 after 10 years as main anchor. She now works on shows for CBBC
On June 10, 2008, Wilkinson announced her engagement on-air.
Wilkinson joined Steve Backshall on CBBC and BBC2 presenting Live 'n' Deadly in 2010. In 2012, she joined the Ed Petrie vehicle All Over the Place for its second series on CBBC as well as Marrying Mum and Dad in which she also presents with Ed Petrie. Wilkinson currently presents a nature documentary for children on CBBC called Naomi's Nightmares of Nature. Naomi also co-presents CBBC's "Wild and Weird" with Tim Warwood. In 2015 Naomi was one of the judges on the Countryfile photographic competition.
Wilkinson has been a television presenter since 1999. She started work on Milkshake for Channel 5 in 2000 where she was producer and presenter. She has been a regular presenter on CBBC since 2010 after leaving Milkshake - she has her own show: Naomi's Nightmares of Nature.
In 2013 & 2014 she presented a live show called WILD on CBBC. She is currently filming All over the place: Asia; Wild and Weird series 2; Marrying Mum and Dad series 5 and Naomi's Nightmare of Nature series 4.
Naomi is one of nine presidents of The Young People's Trust for the Environment.