The conducting repertoire of Paul Phillips includes over 1000 works conducted in performance, encompassing much of the standard orchestral repertoire as well as numerous operas, musicals, ballets, oratorios, cantatas, and contemporary works. He has conducted all of the numbered symphonies of Beethoven, Schubert, Schumann, Brahms, and Tchaikovsky; the complete London symphonies of Haydn; the late symphonies of Mozart, Mendelssohn, and Dvorak; and most of the orchestral music of Mahler, Sibelius, Ravel, Debussy, Bartok, Respighi, Stravinsky, and Copland, among others.

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As the winner of 11 ASCAP Awards for Adventurous Programming, Phillips has conducted more than 75 world and US premieres. His vast repertoire of 20th- and 21st-century music includes works by John Adams, Leonard Bernstein, William Bolcom, Valerie Coleman, Lukas Foss, Gabriela Lena Frank, Jennifer Higdon, Philip Glass, Adolphus Hailstork, Christopher Rouse, Kaija Saariajo, and Steven Stucky. Phillips has also conducted many of his own compositions and championed the music of Anthony Burgess and William Perry, with numerous performances, premieres, and recordings of their music.