He graduated from the Prague Conservatory (1982, the class of Professor Ilja Hurník) and from the Music Academy of Arts in Prague (1989, the class of Professor Jiří Pauer). Since 1986, he's been teaching composition and music theory at the Prague Conservatory; in 1992, he assumed the position of deputy director, and in December 2004 became the headmaster. He is a member of the Czech Composers Society, the chairman of "Přítomnost" association for contemporary music (until 2005), and the vice-chairman of "Collegium 2001".
As a composer, he has received a number of awards, for instance an honorable mention at the "Generace '84" competition for his Violin Sonata, or second prize award for his Musica Per Archi (Generace '86); his Concerto for Violin and Orchestra was chosen for the semifinal of the composer's international competition in London, The Concerto Prize 1990, at which he participated along with the violinist Jaroslav Svěceny. Many of his compositions were recorded for broadcasting companies as well as to be published on CD, and have been performed at festivals of contemporary music. Numerous pieces were chosen as compulsory compositions at prestigious performance festivals. Some of them were premiered abroad, such as Astoriana in 1998 - variations on the theme by Astor Piazzolla for a string orchestra, or the orchestral piece A Tribute to the Cathedral of Trento in Italy. The extensive Missa Solemnis for solo singers, mixed choir, organ and orchestra is dedicated to the Charles University in Prague. Another of Trojan's vocal instrumental piece, the opera-musical called "Bylo nás pět" /There Were Five of Us/, which was inspired by the famous Czech literary work by Karel Poláček, was staged by the Children's Opera of Prague and was successfully performed at the music festival Prague Spring 2003 in co-operation with the Prague Conservatory. His Cantabile and Capriccio for Violin and Piano, composed in the year 2000 for the Mozartiana luventus festival, has already becomne widely included in the repertoire, his latest composition for the same ensemble - Five Romantic Pieces (2014) was perfomed by the members of Czech Trio -  violinist Dana Vlachova and pianist Milan Langer.
Interweaving of dance elements with classical music, a feature that is to be found in a number of Trojan's recent compositions, informs significantly both the structure and content of his Dancing Quartet, which was successfully premiered by the Apollon Quartet at the Borderlines of Music and Poetry festival in the year 2005. Pavel Trojan also works for film. He is, for instance, the author of the music score for the film Nepočestná, directed by J. Krejčík.
He regularly appears on juries at performance or composition competitions (e.g., Hořovice 1996, Castelfidardo 1998, 2000, 2002 and 2004). He is also the author of a textbook entitled Selected Examples in Harmony.