FLCL has a sequel...

FLCL Progressive and Alternative Combo Trailer

The sequel anime series was announced on March 24, 2016 via the Toonami crew's Tumblr and Facebook page that 12 new episodes of FLCL would be produced in cooperation with Production I.G. The upcoming episodes will be split into two individual seasons: FLCL Progressive (フリクリ プログレ Furikuri Purogure, "FLCL Progress") and FLCL Alternative (フリクリ オルタナ Furikuri Orutana, "FLCL Ortana") which will serve as sequels to the popular series which was broadcast on Adult Swim's anime block in 2003. 

The crew includes Neon Genesis Evangelion character designer Yoshiyuki Sdamoto and original series director Kazuya Tsurumaki. The sequel series Progressive will premiere on Adult Swim’s Toonami programming block on June 2, 2018. In the United States, FLCL Progressive will air in June, and FLCL Alternative will air in September  In Japan, the premiere will be divided into two theatrical showings, with FLCL Alternative releasing in September 7, 2018 and FLCL Progressive in September 28, 2018.

The official synopsis of the series was published by Adult Swim:

In the new season of FLCL, many years have passed since Naota and Haruhara Haruko shared their adventure together. Meanwhile, the war between the two entities known as Medical Mechanica and Fraternity rages across the galaxy. Enter Hidomi, a young teenaged girl who believes there is nothing amazing to expect from her average life, until one day when a new teacher named Haruko arrives at her school. Soon enough, Medical Mechanica is attacking her town and Hidomi discovers a secret within her that could save everyone, a secret that only Haruko can unlock.

But why did Haruko return to Earth? What happened to her Rickenbacker 4001 she left with Naota? And where did the human-type robot 'Canti' go?

Production I.G vice president Maki Terashima-Furuta announced at the annual 2016 Anime Expo that original series character designer Yoshiyuki Sadamoto would be reprising his position for the upcoming sequel and that Psycho-Pass director Katsuyuki Motohiro would be supervising the production. Additionally, it was announced that Japanese alternative rock band The Pillows would be returning to provide the musical score for the anime.