Kanji Sasahara is an introverted college freshman just looking for a place to fit in. One day, he happens to stumble upon the club known as the Society for the Study of Modern Visual Culture—otherwise known as Genshiken—that serves to bring the full spectrum of otaku culture together. His first visit to the club, however, does not end well as Sasahara's pride is crushed by his senior, Harunobu Madarame, and he leaves the meeting in full denial of his otaku nature. However, after befriending club member Makoto Kousaka, who turns out to be a hardcore otaku despite his looks, Sasahara becomes more involved with club activities which include obsessing over their favorite anime, reading doujinshi, and attending conventions. There, he meets other interesting people like Kousaka's vehemently non-otaku girlfriend Saki Kasukabe, who strives to turn her boyfriend into a "normal guy."

While Saki struggles to understand otaku culture and her boyfriend's love for it, Sasahara finds himself enjoying his time at Genshiken, gradually shedding any denial he once had about being an otaku and immersing himself in an otaku lifestyle.