In 1990, Trojan’s Concerto for Violin and Orchestra, performed by violinist Jaroslav Svěcený advanced to the semifinals of the composition-interpretation competition The Concerto Prize in London. Four Waltzes for Piano (1982) were performed at the Days of Contemporary Music festival in 1994, and a year later the Piano Trio (1995) was performed here. Trojan’s cycle of etudes for accordion Days (1994) was awarded in Castelfidardo, Italy (1995).

In 1998 the composer completed the extensive Missa solemnis for soloists, choir, organ and orchestra, which is dedicated to Charles University. This spiritual vocal-instrumental composition was premiered in 2008 at a gala concert in Dvořák’s Rudol fina Hall, held on the occasion of the 200th anniversary of the foundation of the Prague Conservatory and the 660th anniversary of the foundation of Charles University.
Many of Trojan’s compositions are dedicated to the accordion or ensembles containing this instrument. Most of these compositions were written  at the initiative of Ladislav Horák, a leading Czech accordionist and Trojan’s colleague at the conservatory. These include Variations on a Theme by Astor PiazzollaAstoriana from 1998, which were first written for solo accordion, later adapted for various ensembles and are one of the author’s most frequently performed compositions.

Commissioned by Mozartian Iuventus in 2000, he composed Cantabile a capriccio for violin and piano. A year later, in Trento, Italy, Trojan premiered his composition for orchestra Omaggio al Duomo diTrento  (Tribute to Trento Cathedral).

In the work of Pavel Trojan, instructional and children’s works are significantly represented. This includes, inter alia:  cycles for young pianists Miniatury, Kontrasty, Album for Youth or the cycle Střípky(Fragments, 1999) to words by Jiří Žáček (premiered at Days of Contemporary Music 2002) for children choir. The most extensive achievement in this area, however, is the children’s opera There Were Five of Us (2000–02; libretto by Marie Kronbergerová) based on the motifs of the Czech writer Karel Poláček. It was presented as part of the Prague Spring Festival 2003 in co-production between the Prague Conservatory and the Prague Children’s Opera.

Trojan’s composition Capriccio for brass and organ (2002) was performed at the Days of Contemporary Music in  2003, and the Touches of Poetry festival in 2004 premiered the  composition Dancing Stringsperformed by the Apollo Quartet. In 2006, Variations on the  Theme and Honour of Václav Trojan(composed on the occasion of the centenary of Václav Trojan’s birth) was created. The Sinfonia giocosa (2008) was written for the Pilsen Philharmonic at the initiative of conductor Jiří Malát and was premiered at the Prague Premieres Festival in 2008.  In 2009 he composed Piano Trio No. 2 for the Czech Trio.

Trojan’s works are often created at the instigation of leading artists. For example, the Concerto for Violin and Orchestra No. 2 (2015) was composed for Jiří Vodička, concertmaster of the Czech Philharmonic, the Concerto for Recorder   (2018)  was  written at the initiative of Jakub Kydlíček,  and Trojan’s latest concert composition Concerto for Oboe and Orchestra “Eiger” was requested  by Vilém Veverka.  

An important area of Trojan’s interest is musicaland dramatic work. In addition to the already mentioned opera There Were Five of Us, there is the opera Shepherd’s Tale from 2012, whose libretto was created by the author’s adaptation of the original libretto by Ascanio Ordeia from the end of the 16th century for the madrigal opera The Faithful Lovers by Guasparro Torrelli. The Shepherd’s Tale was rehearsed and performed by the singing department of the Prague Conservatory as part of the Prague Spring 2013 festival.

The composer also intervened in the musical genre. Based on a libretto by Gustav Skála, he created (2016) the original Czech musical Závišův kříž (Závišův kříž) (2016)  on a theme from Czech history about the “forbidden love” of the knight Záviš of Falkenštejn and Queen Kunhuta.

Trojan is also the author of a number of compulsory compositions of major international competitions. For example, for the senior category of the World Competition in Castelfidardo in 2006 he created the obligatory composition  Capriccio for accordion and for the 59th International Music Competition Prague Spring 2007 the composition Solo for French Horn.

Trojan’s compositions have been released on a number of CDs and more than twenty of his works have been recorded on Czech Radio. Trojan’s compositional activities also include incidental and film music.

The composer is often invited to the juries of major interpretation and composition competitions, e.g., to Castelfidardo, Italy (World Accordion Competition), the international competition “Societa’ Umanitaria Competition” in Milan. He is the chairman of the jury of the Antonín Dvořák International Composition Competition organized by the Prague Conservatory in cooperation with Seouloratorio, a Korean musical institution that interprets and promotes Dvořák’s works in the Republic of Korea.

He is a member of the Society of Czech Composers, was a long-time chairman of the association for contemporary music Přítomnost, was a member of the composers’ association Harmonie.

Since 1986 he has been active at the Prague Conservatory, first as a teacher of music-theoretical subjects, and since 1991 as a composition teacher. From 1992 he held the position of deputy headmaster, from December 2004 to August 2018 he was the headmaster of this school. He is currently a composition teacher there.

As the director of the Prague Conservatory, he pushed through the construction of a new Concert Hall of the school with a capacity of more than 300 spectators (opened in 2011), the Theatre Hall Theatre Na Rejdišti (opened in 2010) and the overall modernization of the teaching space. He introduced new fields (saxophone, harpsichord, recorder), founded the school baroque orchestra and orchestra focused on the interpretation of contemporary music (Prague Conservatory Modern).

In connection with the celebration of the bicentenary of the founding of the school, he renewed the Union for the Enhancement of Music in Bohemia, an association that founded the conservatory and financed and managed for more than a hundred years. The renewed Unity supports the students of the Prague Conservatory and helps them especially at the beginning of their concert activities