Charli D'Amelio, from Norwalk, Connecticut, hit the milestone after a year and a half on the app.
It comes days after a controversy over her behaviour in a YouTube video.
In the first episode of her family's reality series, Dinner with the D'Amelios, fans claimed the star acted disrespectfully toward the personal chef who prepared them dinner.
More than 600,000 fans swiftly unfollowed her in protest.
However, controversy died down after D'Amelio shared a video in which she apologised for her actions, and promised to do better.
She took to Twitter to thank fans for her record-breaking achievement on Sunday: "100 million people supporting me... I truly cannot believe that this is real," she wrote.
The 16-year-old started out - as many did on TikTok - sharing videos of herself dancing in her bedroom.
Her profile both on TikTok and outside the platform, has rocketed in the last year. She became the first person to hit 50 million subscribers in April.
She made her film debut in the 2019 animated feature Stardog and Turbocat, voice-acting alongside Luke Evans, Bill Nighy and Gemma Arterton.
The TikTok star has collaborated with global brands on fashion and make-up lines, and also had a drink named after her at Dunkin' Donuts.
Her first book, Charli: The Ultimate Guide To Keeping It Real, will be released later this year.
According to Forbes, such deals have earned her an estimated $4 million in the last year alone.
D'Amelio found herself at the centre of another controversy earlier this year when she was falsely credited with creating the "Renegade" dance trend - something which actually came from Jalaiah Harmon, a black teenager from Atlanta, Georgia.
While D'Amelio had never claimed to have created the dance, the confusion sparked claims that TikTok's algorithm showed unintentional racial bias.