The Reclaim Party candidate received 47,634 votes, finishing in sixth place.
Candidates have to achieve five per cent of first-preference votes to have the money returned.
Lib Dem candidate Luisa Porritt has also lost her deposit after getting just 4.4 per cent of the votes.
The money – likely to total £160,000 or £170,000 – will be retained by London Elects and used to offset the costs of running future elections.
In March, Mr Fox told the Standard that his campaign was being funded solely by the millionaire financier Jeremy Hosking, a former Tory donor who has also funded the Brexit party.
After his defeat, the actor and “anti-woke” campaigner tweeted: "Thank you so much to the 47,634 of you who voted for me. I am profoundly moved. Sleep well".
Labour’s Sadiq Khan won a second term as London mayor after securing a victory over Shaun Bailey.
Mr Khan polled 1,206,034 votes, compared with 977,601 for his Tory challenger.
This gave Mr Khan a majority of 228,433, the second-highest on record.
He holds the records for most votes (1,310,143) and the biggest winning majority (315,529) from his inaugural victory in 2016 against Tory candidate Zac Goldsmith.
Mr Khan will serve a further three years. The normal four-year term has been shortened after the election was delayed a year due to the pandemic.
Following his win, Mr Khan said: "I want to say thank you from the bottom of my heart.
"I am deeply humbled by the trust Londoners have placed in me to continue leading the greatest city on earth.
"I promise to strain every sinew, help build a better and brighter future for London, after the dark days of the pandemic and to create a greener, fairer and safer city for all Londoners, to get the opportunities they need to fulfil their potential.
"I am proud to have won an overwhelming mandate today."