On January 25, 1860, he was elected President pro tempore of the State Senate (83rd Session).
From 1860-1861, Senator Nathan Lapham resided in his home (the Nathan Lapham Home) in Peru, New York where he was part of the Underground Railroad feeding and sheltering fugitive slaves escaping to Canada.
An Historic Marker was erected in 2010 by the Town of Peru at his then homesite.
Later he married Hannah Barker, a niece of his first wife, and they had several children.
He was buried at the Quaker Cemetery in Au Sable, New York.