High school is home to all kinds of new encounters and people, but for Renge Ooyama, her first encounter with a classmate was much weirder than she expected. When Renge meets her classmate Sumire Yotsuya, the latter is clearly not the 16-year-old student she claims to be, but instead is a wooden puppet operated by an old man dressed in black. Though the students and faculty attempt to ward off the man, he refuses to break character and only gives confused responses from the puppet Sumire. Thanks to the principal seeing Sumire as a real girl, teachers and pupils alike must accept this new and odd student as the normal person "she" claims to be.

Now classmates with Sumire, Renge is creeped out when "she" insists they hang out and become friends, and worries how it might affect her reputation at school. However, when Renge falls into trouble, it's none other than Sumire who comes to her aid. Finding that Sumire (and the old man) aren't so bad after all, she decides to give "her" a shot.

Sumire♡16-sai!! follows Renge and her schoolmates as they attend school with this masquerader and come to realize that despite the wooden body, Sumire's heart is certainly real.