The previous record was 38,262 which was set at the Tottenham Hotspur Stadium in the 2019 north London derby. Ticket sales for Saturday's match had already surpassed that figure on Sept. 1, Arsenal announced.
Arsenal also confirmed that 53,757 tickets were sold for Saturday's derby.
Kelly Simmons, The English FA's director for the Women's Professional Game, said: "After a stunning summer that saw packed out stadiums to watch the Lionesses during the UEFA Women's Euro, we were really confident that we'd see a new record attendance early on in this season's Barclays Women's Super League.
"The atmosphere at The Emirates was absolutely incredible, and seeing 47,367 fans in the stadium shows just how much the women's game has grown. I am delighted that we have seen such big interest in the league since the start of the season, which is great credit to the clubs.
"I hope this momentum can continue throughout the whole campaign and I encourage anyone to come along to a Barclays WSL match and be a part of this exciting league."
Arsenal had sold over 50,000 tickets for the match before Saturday and Arsenal manager Jonas Eidevall said that he is keen to see attendances for women's matches continue to rise.
"It's 50,000 sold tickets," he said. "It's not giveaways, it's not sold for a discounted price -- it's sold tickets.
"I think that's really really special because that means that doing this the way the club has done it, it's sustainable. It shows the interest there, it is for real.
"The investment that we as a team, the club has done but also all the past generations and past teams before us have done to put us onto this stage here, that's phenomenal.
"So we feel that, of course we want to go out and make the most of it so it can happen again more frequently."
Eidewall's side will also play their Champions League group stage matches at the Emirates if they beat Ajax to qualify.