In January 2016, Nayoung, Sejeong and Mina were introduced as Jellyfish Entertainment's first female trainees on the Mnet survival show, Produce 101, where 101 female trainees from various companies competed to debut in an eleven-member girl group that would promote for a year under YMC Entertainment.

Despite denying earlier reports of Sejeong and Mina debuting in a 3-member girl group in June, Jellyfish Entertainment confirmed on June 7 that the two I.O.I members would debut within the month in what would be the company's first girl group.

[3][4] Because of YMC Entertainment's special terms in which I.O.I's members are allowed to do activities under their respective companies while I.O.I was on break or while the group promoted in sub-units, there were no complications with the plan.

[13] Gugudan participated in Jellyfish Entertainment's annual winter project, Jelly Christmas 2016, with their label mates Seo In-guk, VIXX, Park Yoon-ha, Park Jung-ah, Kim Gyu-sun, Kim Ye-won and Jiyul.

[22] On May 17, it was announced that youngest member Hyeyeon would go on a temporary hiatus from all the group activities due to health issues.

[23] Gugudan officially debuted in Japan with a release of their first Japanese single Stand By on September 19.

[30] In July 2017, Jellyfish Entertainment formed the subunit group named Gugudan 5959 (Korean: 구구단 오구오구; spelled as "Ogu-ogu"), composed of the youngest members Mina and Hyeyeon.

Gugudan SeMiNa debuted with the release of their self-titled single album consisting of two tracks on July 10, 2018.