The sermons used to be served in the open air on the elevation beyond the crossing over the Teplá Vltava. A chapel consecrated to Virgin Mary was built here in 1714 but it soon became insufficient for the needs of the village. That is why it was rebuilt into a small church in 1724. Construction works nevertheless still continued after the church consecration. The altar painting of the church patrons St. John of Nepomuk and the Holy Family as well as the painting of the Holy Spirit were ordered by Adam František Schwarzenberg from Pietro von Roy in 1724 and 1725. The organ builder Jiří Dvorský built the positive in 1727 for 150 guilders. A year later the church tower with two bells was completed. After completion of construction works, the chaplaincy was promoted to the parish. The floor was covered with planks in 1829. The fees per each seat were introduced in 1833-1841 and later also the fees from participation in the church service.
Local vicar had to wait for an assistant till 1853, when a subsidy for a chaplain was established due to high number of parishioners. Wenzel Bayer became the first chaplain of the church starting 12th July of the same year. Further extension of the church was considered and eventually carried out in 1859. The pseudo-Baroque pulpit originates from this rebuilding. At that time, the third bell had been suspended in the wooden turret since 1770 and the tower clock had indicated the time since 1842. The current clockwork mechanism from 1914 was made in the Vienna shop of Richard Liebing. The first thing any visitor of the church notices is its beautiful cristal-cut chandelier - a reminder of the renowned era of the Lenora glass-works. The first chandelier was donated to the church in 1862 by the glass-works owner named Kralik. This nevertheless fell down after forty years of service, which is why a new one was made in the same glass-works in 1902 that has been illuminating the church to date. Both window-panes depicting the evangelists John and Matthew were also made in the Lenora glass-works. The original organ unfortunately has not been preserved. The church nevertheless today boasts of the instrument that was declared a Cultural Monument and is a work of the Tachov organ builder Gartner from 1812. The church of Horní Vltavice witnessed many interesting events: in 1957 a regular marriage of the main characters of the classical film fairytale "The Proud Princess" - the actors Vladimír Ráž and Alena Vránová; the sons of the National Artist Zdeněk Štěpánek, the actors Martin and Petr Štěpánek, served here as acolytes in their childhood.