Willow Glen began as a marshy area with numerous Willow trees surrounding the Los Gatos Creek and Guadalupe River. Much of Willow Glen was laid out by Frank Lewis and Isaac Bird (the namesake of "Bird Avenue"). In 1860, Lewis dug the channel between Willow Street and Curtner Avenue that carries the Guadalupe River to this day. That channel effectively drained the marsh and opened Willow Glen for farming. By the late 1800s, Willow Glen was generally considered one of the most prized locations in all of the Santa Clara Valley for raising wheat, barley, hay, tobacco and hops. By 1880, plots of Willow Glen farmland were priced nearly 10 times higher than similar plots in the valley.

Lincoln Avenue was renamed from "Willow Glen Road" in 1865, shortly after the assassination of President Abraham Lincoln. In 1927 the area was incorporated as the town of Willow Glen. By the 1930's the growth of the community made it necessary to join the City of San Jose and in 1936, the town of Willow Glen ceased to be as it became a part of the City of San Jose.

During the 1960's, Willow Glen was once again faced with an attempt to divide its community with the proposal of an expressway that would run through the center of their neighborhood. Once again, the community joined together to stop this incursion. Today, downtown is a bustling shopping district filled with shoppers, strollers and dogs walking up and down the sweeping tree-lined sidewalks.