The first Orthodox parish in Rahway was organized in 1916 as part of the Russian Orthodox Greek Catholic Church in America, later more commonly known as the "Metropolia". At that time the parish was known as St John the Baptist Church. But in the mid 1960's, after three years of bitter and expensive court battles to prevent the parish from unfairly dismissing Fr Theophil Krehel and seceeding, the Metropolia and a small group of supporters finally lost an appeal. Fr Krehel was dismissed and the parish was received into the Carpatho-Russian Diocese.

Fr Krehel and about 25 former parishioners of St John's met on December 10, 1967 to start a new parish under the name "Holy Trinity." In 1968, the small community moved from Colona Civic Improvement Club to the U.A.W. Hall in Clark, and then to the Abraham Clark School in the same town, where Sunday services were held for the next ten years. Feast days and events (baptisms, weddings, funerals, etc) were held at Holy Comforter Episcopal Church in Rahway. A rectory was purchased in 1969, and then in 1978 a permanent parish home was established with the purchase of the former Christian Science building in Rahway.

Fr Theophil Krehel fell asleep in the Lord on January 16, 1987. Fr Peter Telencio, then serving as a US Army Chaplain at Fort Monmouth, was the interim pastor until Fr John Jillions was assigned in October 1987, after serving a parish in Brisbane, Australia for three years. Holy Trinity Church celebrated its 25th Anniversary in September, 1992. After almost seven years as pastor, Fr Jillions moved to Greece with his family in August, 1994 to continue his education at the University of Thessaloniki. After Fr Jillions moved on, Fr Witalis Suszczenia served the parish until 2008.

Today, two Orthodox parishes continue to exist in the small town of Rahway, but by the grace of God, there is friendly cooperation between priests and parishioners, without the rancor that characterized the early years following the tragic legal battles of the past.