Peirce was born in Dorchester, Massachusetts (now part of Boston) on December 15, 1808. His father was Joseph Hardy Peirce (1773–1832), the son of Joseph Peirce; his mother was Frances Temple. He had at least one brother and five sisters. He attended public schools in Boston, and then about 1822 worked for his father and uncle as a court clerk. On October 24, 1824 he enrolled on the crew of the merchant ship "Griffon" mastered by his brother Marus T. Peirce. On March 25, 1825 the "Griffon" landed in Honolulu for provisions. He was promoted to ship's clerk for the three-year trading voyage on the west coast of British Columbia. In September 1828 the "Griffon" was back in Honolulu, and Peirce stayed while his brother returned.