It was launched in 1964 under the name Bessatsu Shōnen Magazine (別冊少年マガジン).

In 1969 it was retitled as Monthly Bessatsu Shōnen Magazine (月刊別冊少年マガジン) and its publication frequency increased from quarterly to monthly.

After suspension in 1974 it started publishing again, in 1975 it was renamed as current magazine title.

[2] In January 2023, Shōnen Magazine R ceased publication.

[3] In February 2023, a new web publication called Getsu Maga Kichi (Monthly Magazine Base) replaced Shōnen Magazine R.[4]