The choir was founded in 2002 by Tamás Bubnó, a Hungarian church musician and conductor. When he was collecting religious melodies in the Subcarpathian area in the Ukraine for his DLA thesis, entitled: Origin and Variants of Greek Catholic Liturgical Chants in Hungary and the Subcarpathian Area, one day he discovered an unknown manuscript of the Liturgy of St. John Chrysostom for male choir, composed by János Boksay; a Greek Catholic priest and composer at the turn of the century (1874-1940). He decided to gather some of his friends, all professional singers working with the best choirs in Budapest (the Male Choir of the Defence Ministry, Choir of the Hungarian Radio, the National Choir, the Tomkins Vocal Ensemble, etc.) and some of his former students (from the Schola Cantorum Budapestiensis), to perform this work. The choir started to participate regularly in Byzantine liturgical services, mostly in Greek Catholic Churches in Budapest and other Hungarian cities. The ensemble took its name Saint Ephraim, the Syrian (307-378), who was the first great Byzantine hymnographer, called "The Harp of the Holy Ghost" by his contemporaries.

The first CD of the choir, the Boksay-Liturgy that Bubnó discovered, was published by Hungaroton. (2005) Their repertoire was enhanced by some classics of the Slavonic-Orthodox music, documented on their second recording, that appeared on the label Orpheia in 2006. This album is a compilation of Greek-Byzantine, Hungarian and Slavonic ecclesiastical music and it features a rarity: the one and only motet of Ferenc Liszt in Old Church Slavonic (Slavimo Slavno Slaveni). The choir received significant sponsoring at that time from the National Council of the Ruthenian Minority of Hungary. The posterior CDs by the Saint Ephraim Male Choirs, Liszt: Male Choruses I (2009), Liszt: Male Choruses II (2010) and Byzantine mosaics (2010) were released by BMC. The latter received the Supersonic Award by Pizzicato Magazine (Luxembourg) in June 2010.

In 2006 the St. Ephraim Male Choir won the category of Professional Chamber Choir in the 25th Anniversary Competition in the Hajnówka International Festival of Orthodox Music (Poland). They were the first ensemble coming from a non-Slavonic country to win first prize in the history of the competiton.

In the last couple of years they have given concerts in Moscow, St.Petersburg, Berlin, Rome and Paris. They have been invited to the Schleswig-Holstein Music Festival (2007) Donaufest-Ulm (2010) in Germany, Festival de Royaumont (2008) Festival d'Auvers-sur-Oise (2009) in France, Janacek Festival Kravare -Czech Republik (2010) Liszt Festival Raiding (2010), and have toured Poland, Slovakia, Serbia as well. The Saint Ephraim Male Choir has also performed at the most prominent festivals in Hungary: Budapest Spring Festival, (2006, 2008,) Valley of Arts, Kapolcs (2006,2007), Arcus Temporum Festival, Pannonhalma (2008) Miskolc Opera Festival (2007, 2010) Tchaikovsky Marathon, Budapest (2008) 'Ördögkatlan' Festival (2008-2009-2010), Pécs - Cultural Capitol of Europe (2010).

The choir's main goal remains the perform the ecclesiastical music of the Byzantine rite in an authentic way. However, for thematic concerts the ensemble perform other compositions from the Western tradition (Gregorian chants, Protestant songs and gospels), and secular pieces as well, provided they can be performed by a chamber choir. Their concerts of Liszt and Bartók were enormously successful at the Schleswig-Holstein Festival. They have plans to record all male choral compositions of the two great Hungarian composers alongside recording other pieces of Byzantine rite music.