HoneyComing's story revolves around the protagonist Kōichirō Ogata, a male first-year high school student who does not have any interest in matters such as love or romance. The high school he is admitted to, named Aikyō Academy, used to be an all-girl school formally named Aikyō Girl's Academy, and still carries a high population of female students. He starts school with his childhood friend Asahi Kamijō, his younger sister-in-law Mio Ogata, and best male friend Masanori Shinozaki. Kōichirō eventually meets two more female upperclassmen from the same school named Clarissa Satsuki Maezono, and Yuma Shichiri, along with a female underclassman from an affiliated school named Marino Tagaya; Kōichirō becomes friends with them. Since the school used to only have female students, there are certain classes oriented towards girls which are still required to take, such as lessons on love and romance.
These lessons are known as Love-making Lessons, and students at Aikyō are required to take these classes on how to fall in love, and the ways of proper romance techniques. Each lesson, two people (of the opposite sex) pair up to make something, such as a meal for example, and they must form good communication if they intend to pass the test. There are also tests on practical skills which required note taking to later be studied for tests. During these lessons, students from Aikyō, and a nearby affiliated junior-high school, are combined for a total range of six grades from the lowest to the highest. Each time, forty new students from either school are chosen to taken part in a special class for the Love-making Lessons. The students in the special class this year include: Kōichirō, Asahi, Clarissa, Mio, Yuma, Marino, Kaoru, Masanori, and Hiroko. Two teachers are assigned to this class: Ichigo Raidō (who is in charge of the boys), and Tsukasa Kurebayashi (who is in charge of the girls).