He was appointed as a music teacher at the University of Helsinki in 1834. In Helsinki he founded a musical society, a student choir and an orchestra. In 1848 Pacius wrote the music to the poem Maamme by Johan Ludvig Runeberg, which was to become Finland's national anthem. Pacius’s music was also used for the Estonian national anthem Mu isamaa, mu õnn ja rõõm.
In 1852 he composed Kaarle-kuninkaan metsästys (The Hunt of King Charles) which was the first Finnish opera, with a libretto in the style of Romantic nationalism, like the national anthem designed to ensure Finland's Grand Duke (i.e. Russias Emperor) on the total loyalty of his subjects in Finland. The libretto was written by the author and historian Zacharias Topelius in close collaboration with the composer.