The Reclamation Party candidate received 47,634 votes, finishing sixth.
Candidates must get five percent of the first-preference votes to get their money back.
Lib Dem candidate Luisa Porritt also lost her deposit after getting just 4.4 percent of the vote.
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The money, which is likely to be £ 160,000 or £ 170,000, will be held by London Elects and used to offset the costs of holding future elections.
Following his defeat, the ‘anti-awakening’ actor and activist tweeted: “Many thanks to the 47,634 of you who voted for me. I am deeply moved. Sleep well”.
Khan got 1,206,034 votes, compared to 977,601 for his conservative rival.
Sadiq Khan wins second term / PA
This gave Khan a majority of 228,433, the second-highest on record.
He holds the records for the majority vote (1,310,143) and the largest winning majority (315,529) since his inaugural victory in 2016 against conservative candidate Zac Goldsmith.
Khan will be three more years old. The normal four-year period has been shortened after elections were delayed a year due to the pandemic.
After his victory, Khan said: “I want to thank you from the bottom of my heart.
“I am deeply honored by the trust Londoners have placed in me to continue to lead the world’s largest city.
‘I promise to test every nerve, to help build a brighter and better future for London after the dark days of the pandemic and to create a greener, fairer and safer city for all Londoners, in order to obtain the opportunities they need to realize their potential.
“I am proud to have won an overwhelming mandate today.”
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