Born in Prattsburgh, Steuben County, New York, he attended Franklin Academy there. He studied law, was admitted to the bar, and commenced practice in Bath. He was a member of the New York State Assembly (Steuben Co., 1st D.) in 1852, 1857 and 1858. In 1858, he was the Republican candidate for Speaker, but was defeated by Democrat Thomas G. Alvord on the 53rd ballot.
Following the war, he was Acting Commissioner of Indian Affairs in 1865. He was appointed Minister Resident to Japan on January 18, 1866, and remained on the post until November 11, 1869. It was in his role as Minister Resident in Japan that Van Valkenburgh prevented the delivery of the CSS Stonewall to the forces of the Tokugawa clan during the Boshin War.
After his return from Japan, Van Valkenburgh settled in Florida, and was appointed associate justice of the Florida Supreme Court on May 20, 1874. He remained on the bench until his death in Suwannee Springs, near Live Oak in 1888. He was buried at the same cemetery of his wife, Anna Van Aleknburg (née Simpson),[1] Old St. Nicholas Cemetery, on the south side of the St. Johns River, in Jacksonville.