The previous record was $34,440 for a rookie card of former US soccer player Mia Hamm sold in June.
ESPN reported the Williams card was bought by alternative-asset trading platform Alt on behalf of a private client.
Autographed Serena Williams rookie card
"People are accepting women's trading cards as collectables," ESPN quoted Goldin Auctions founder Ken Goldin as saying.
The 40-year-old Williams, who is still hunting a record-equalling 24th Grand Slam title, has not competed since limping out of her first-round match at Wimbledon in August.