In the late 1640's (about 20 years after Peter Minuit bought Manhattan Island), Adriaen Van der Donck received grant of land from the Dutch East India Company which he called Colon Donck ("Donck's Colony"), and built one of the first saw mills in the New World at the junction of the Hudson and Nepperhan Rivers. Van der Donck was referred to as Jonk Herr ("young Gentleman" or "young Nobleman") by reason of his status in Holland, and these words evolved through several changes to the Jonk Heer's land and The Younckers, The Yonkers and finally to the present Yonkers. The area acquired by Van der Donck passed into the hands of the Philipse family in the latter part of the 17th century, and Philipse Manor Hall was erected at this juncture of the two rivers in the early 1680s. Yonkers' strategic location fostered its development into a major trading center and its early settlers (including Native Americans, English and Dutch) created a diverse community. Yonkers was a small farm town in the 1700's but many businesses soon began to emerge: the saw mills and grist mills multiplied, land development increased, and blacksmith shops, taverns, and general stores came into being. The waterfront still remained the key, providing pause for sloops and stagecoaches. Innovations in travel - via both land and water - accelerated the development of the industrial era in Yonkers, and the first railroad station (built in 1848 on the site of present day Yonkers Station) contributed to more occupations and trade.

A stone mill (possibly the city's first industrial site) was built during 1805 -14 in the Tuckahoe area of Yonkers. It was used as a cotton factory until 1852 when the Hodgman Rubber Company bought it, and thus began yet another industry. Yonkers innovators such as Elisha Otis created the first safety elevator and Yonkers became a center for carpet and hat manufacture, in addition to establishing the first sugar industry in 1862. And in 1867, the first elevated mass transit system in the world was created in Yonkers.

The Village of Yonkers (then extending approximately two miles along the Hudson River) was incorporated on April 12, 1872 with a population of approximately 7,500. On June 1, 1872, Governor Hoffman signed the charter establishing Yonkers as the first in Westchester County to be incorporated and designated as a city. The population had grown to about 20,000 by that time, and today there are nearly 200,000 people residing in Yonkers.