The wooden church was rebuilt in 1645 and later in 1720, at which time it was given the name of the Holy Trinity. By the mid-19th century, the wooden church had deteriorated. Thanks to the efforts and funds of the parish priest Father T. Šimanskis and the parishioners, the construction of the current brick church in Linkmenys began in 1885, based on a design by military engineer Čerkasov. The new brick church was completed, furnished, and consecrated in 1887. In 1898, the church was surrounded by a new brick fence. Linkmenys Holy Trinity Church is an original 19th-century stone and brick masonry building with eclectic and neo-Romanesque features. The church has a
rectangular plan, is basilican, and has a single tower. The churchyard fence is made of stone masonry with plastered pillars. The church's interior is characterized by its simplicity. In the churchyard stands a stone sculpture of a sorrowful Jesus, dedicated to those who died for their homeland and those who perished in exile. There are also wooden chapels commemorating the 600th anniversary of Lithuania's Christianization (1387–1987) and the 500th anniversary of St. Casimir's death (1484–1984). In 2009, a sculpture of Jesus was erected to mark the millennium of Lithuania's name, and in 2010, a sculpture of the Virgin Mary was placed at the main church gate.