The Sullivan Expedition of 1779 passed through the area.
The town's first settler, Green Bently, purchased and developed farmland on the site of the village in 1798. The community was once known as "Millvale" after the village was laid out in 1825. The name was changed to "Millport" in 1829 to recognize its new status by the canal.
The former Chemung Canal passed by the village, raising the population about 1,000. Catharine Creek flows past the village.
In the 1840s, several epidemics reduced the population of Millport.