Emerson attended the Parsonfield Seminary and Effingham Academy. He originally planned to be a doctor, but his love for music persuaded him to pursue a career as a musician. He studied under Isaac Woodbury, a popular teacher at the time. After several years of study in voice, piano, and organ, he moved to Salem, Massachusetts, began teaching, and took charge of his first choir, at the salary of $100 per year. By 1853, he felt confident enough of his abilities to show his music to the public. The Romberg Collection was subsequently published, but found little market.

After eight years in Salem, Emerson moved to Boston, Massachusetts, accepting the position of organist and musical director at the Bulfinch Street Church. In 1857, he became associated with the Oliver Ditson publishers in Boston.

Eventually, Findlay College in Ohio awarded Emerson the degree of Doctor of Music. His works include: