The photo-sharing site, releasing its figures for the year so far on Thursday, found that young female celebrities were the most adept at the platform.
Gomez had more than 103 million followers, more than any user except Instagram itself, which selects intriguing postings from around the world.
The 24-year-old edged out fellow pop singer Taylor Swift, who has just under 94 million followers and was 2015's top star on Facebook-owned Instagram.
A photo posted by Selena Gomez (@selenagomez) on
Following them were two more singers -- Ariana Grande and Beyonce -- and then reality television star Kim Kardashian.
The most followed man -- at number six among celebrities -- was Portuguese soccer star Cristiano Ronaldo.
Gomez dominated Instagram on a topsy-turvy year for the star who cut short a tour as she fought depression brought on by her struggle with lupus.
She re-emerged in November for the American Music Awards, where she urged fans to be true to their inner feelings and said: "I don't want to see your bodies on Instagram."
Gomez also had a high-profile Instagram feud in 2016 with her ex-boyfriend Justin Bieber who quit the platform amid heated exchanges.
The Canadian singer recently said on stage in London: "Hell is Instagram."
Gomez was behind eight of the 10 most liked celebrity photos and seven of the top 10 celebrity videos for the year.
In a finding sure to delight advertisers who target social media, Gomez's most liked photo on Instagram was a promotion for Coca-Cola.