The name of the city probably has its origin in the name of a boyar family called Botaș, whose name can be found in old records from the time of Prince Stephen the Great (late 15th century) as one of the most important families of Moldavia, records which trace it back to the 11th century.
Botoșani is first mentioned in 1439, in which one chronicle says that "the Mongols came and pillaged all the way to Botușani". The town is then mentioned only during the conflicts between Moldavia and Poland: several battles were fought near the town, in 1500, 1505 and 1509. During the reign of Petru Rareș, the town was set ablaze by the Poles. It was during his reign then that we know that the town had a hill fort.
In the 15th century, it was still not a fully-fledged town, but archeological evidence shows that it was a pre-urban settlement. During the second part of the 14th century, some Transylvanian colonists (most likely German or Hungarian) settled in Botoșani. Additionally, a large community of Armenian traders settled in the 14th or 15th centuries.
At the junction of several commercial roads including the "Moldavian Road", which linked Iași to Hotin, the city was initially a market town. By 1579 it already had "the biggest and the oldest fair of Moldavia".
A large Jewish community was established in the city during the 17th century.