Pereslavl-Zalessky was founded in 1152 by Prince Yuri Dolgoruky. In 1175–1302, the town was the center of the Principality of Pereslavl (Zalessky). In 1302, the town became a part of the Grand Duchy of Moscow. Pereslavl-Zalessky had been devastated numerous times by the Mongols between the mid-13th century and the early 15th century. In 1611–1612, it suffered from the Polish invasion.

The history of Pereslavl connected to two of the greatest rulers of Russia of all times.In 1220 one of the most popular ancient Russian heroes Prince Alexander Nevsky, a general, a politician, a saint, was born there. He defended Russia from the two biggest perils at the time when it was at the verge of disappearance from the map and history. He defeated the Swedes and Teutonic knights pushing into Russian territory from the West and concluded an uneasy peace with the then invincible Mongols who devastated most of Russia few years earlier, destroying most of her cities

In 1688–1693, Peter the Great built his famous "fun flotilla" on Lake Pleshcheyevo for practicing navigation and training ship crews, including the so-called Peter's little boat, which would be considered the forefather of the Russian fleet. The Botik (small boat) museum chronicles the history of the first Russian fleet and keeps one of the original model boats.