The allrounder blasted an unbeaten 51 from only 16 balls at North Sydney Oval on Wednesday.
Flintoff broke the previous mark - 22 balls - by smashing a six off the final ball of the innings to push the Stars to 5-186 after the Strikers elected to field first.
The 19-year-old's blistering career-best knock consisted of six fours and three maximums.
Flintoff had not been required to bat in the Stars' past three matches, but her most recent innings was an unbeaten 40 against the Perth Scorchers on October 20.
Australia allrounder Ashleigh Gardner and South African Lizelle Lee shared the previous record for fastest WBBL 50, with both reaching the mark in the same game back in 2017.
No.5 Alice Capsey (49) and opener Lauren Winfield-Hill (47) also played important roles in the Stars' big total.
Flintoff's matchwinning knock proved too much for Adelaide to overcome, with the Strikers finishing their 20 overs on 8-164.
Australia star Tahlia McGrath's troubling run with the bat continued, with the Strikers captain out for one following two ducks in as many games.
Adelaide had solid contributions from Katie Mack (47), Bridget Patterson (41) and Laura Wolvaardt (30) as Sasha Moloney (4-24) was the pick of the Stars bowlers.
It was just the Stars' second win of the tournament, with Adelaide to remain in third on the table with four victories.
Meanwhile, the ladder-leading Sixers trumped crosstown rivals the Thunder by 15 runs in the Sydney Smash thanks to an outstanding all-round display from Ashleigh Gardner.
Gardner hit a vital 52 to rescue the Sixers from 2-7 to 6-163 after they elected to bat first.
Captain Rachael Haynes (37) and No.5 Chloe Tryon (32) attempted to push the Thunder towards an unlikely win, but it was all Gardner.
The 25-year-old opened the bowling to finish with figures of 3-25 to be the clear player of the match.
Lauren Cheatle also picked up three wickets for the Sixers as the star-studded group in Magenta went a game-and-a-half clear on top of the ladder.
The Sixers will battle the Scorchers in Perth on Saturday in a blockbuster top-of-the-table clash.
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