The Bovina United Presbyterian Church, the town's oldest institution, started life as the Associate Presbyterian Church of Delhi.  The congregation was organized in  October 1809, after several pleas from the mainly Scottish settlers in the area for a church.  Alexander Bullions had come to preach in 1807 in response to these pleas and organized the congregation two years later.  The church did not have a regular pastor until 1814, when Rev. James Laing accepted the call.  In 1815, the name of the congregation became the Associate Presbyterian Church of the Little Delaware and after the creation of the Town of Bovina in 1820, it became the Associate Presbyterian Church of Bovina.   In 1859, the congregation received its final name change when it became the United Presbyterian Church of Bovina. 

The congregation over its 200 years has had over 2000 members, 21 pastors, over 100 elders and two church buildings. The first regular church building for the congregation was built at what is now Reinertsen Hill road in 1815.  The cemetery for the church still exists.  The building was in use for over 35 years before it was decided that the size of the congregation merited a new building.  In 1849, the congregation built a larger church in the hamlet of Bovina Center, then called Brushland.  It was expanded in 1859 to hold between 600 and 700 people. 

The congregation's second and third ministers had the longest tenures in the church's history.  Scottish native John Graham came to Bovina in 1832, barely a year after arriving from Scotland, and stayed for 21 years.  His successor, James B. Lee, was the church's longest serving pastor, serving for 32 years.  Reverend Harvey McClellan was pastor for 11 years in the 1930s, leaving in 1942 to accept a call as a military chaplain. In 1985, the church marked a milestone with the installation of its first female pastor, Rev. Karen Patricia. 

The congregation celebrated its Centennial in October 1909, with several days of events.  The 125th, 150th and 175th anniversaries were all observed with events and  special worship services.  On October 10 and 11, 2009, the United Presbyterian Church of Bovina celebrated its Bicentennial with the unveiling of a historic marker, a picnic at the site of the original church, a history program and a special Sunday service, followed by a luncheon.