Lee gained increased popularity after starring in the family drama The Gentlemen of Wolgyesu Tailor Shop (2016), where she received favorable reviews. Her and co-star Hyun Woo were dubbed asThe Ahchoo Couple by fans. Lee also won the Best New Actress award in the television category at the Baeksang Arts Award for her performance.
In 2017, Lee starred in her first leading role in free-to-air TV station with KBS2's youth drama Hit the Top. She was also cast in the web series How Are You Bread alongside Suho of Exo. Lee then starred in the fantasy romantic comedy drama A Korean Odyssey by the Hong sisters, and was praised for her portrayal of three different characters. In 2018, Lee played her first film leading role in mystery thriller Duck Town.