In 1890, distinguished preacher and church leader Edward Judson initiated construction of Judson Church as a memorial to his father Adoniram Judson, the first American foreign missionary. Edward envisioned Judson Memorial as an institution to serve the burgeoning immigrant population of Lower Manhattan through health, nutrition, education, and recreational programs. Backed by John D. Rockefeller and other prominent Baptists of the time, Edward Judson commissioned the leading artisans of the American Renaissance—architect Stanford White, stained glass master John La Farge, and sculptor Augustus St. Gaudens—to create a splendid edifice where the "classes" and the "masses" could meet on common ground.

Toward the end of Edward Judson’s life, it was apparent that the "classes" were none too keen on rubbing shoulders with the immigrant poor, but his dream that is Judson Memorial persisted. The church continued to offer distinctive healthcare and outreach ministries throughout the 1920s and '30s. After the Second World War, visionary ministers like Robert Spike and Howard Moody redefined the idea of what a church could and should be. Beginning in the mid-1960s, Reverend Moody and composer Al Carmines secured for Judson a national presence, opening the church to experimental, avant-garde artists from many genres—dance, painting, theatre—and themselves organized around issues of civil rights, free expression, abortion rights, and the decriminalization of prostitution. More recent Church staff, including Minister Karen H. Senecal, have initiated new programming that seeks to respond to the gentrification of the West Village and related pressures to remove "undesirables," rising homelessness throughout the city, and the growing divide between the "haves" and "have nots" in the New Economy. Over the past decade, Senior Minister Peter Laarman (1994-2003) and other clergy staff have been working to guide the congregation through ongoing generational change and have been actively addressing the deferred maintenance issues in Judson's aging buildings as well.