Pixley was born in Westmoreland, Oneida County, New York. As a youth, he worked on the family farm and was first educated in the village academy, later at the Quaker school in Skaneateles (town), New York. He graduated from Hamilton College and studied law in Rochester, New York, he worked in the law office of Smith, Rochester and Smith. In 1847, he went to Michigan where he was admitted to practice law and qualified to appear before the state supreme court. Two years later he travelled to California during the Gold Rush, and spent two winters working mines on the Yuba River. He met and, in 1853, married Amelia Van Reynegom, daughter of Captain John and Margaret Van Reynegom, who had arrived to San Francisco in 1849 aboard her parents’ ship the "Linda". The Pixleys lived in the North Beach area of San Francisco.