Farnsworth organized the 8th Illinois Cavalry at President Abraham Lincoln's direction and was commissioned its first colonel. He helped secure a lieutenant's commission for his 24-year-old nephew Elon John Farnsworth, who would die in action at the Battle of Gettysburg. The older Farnsworth also was instrumental in raising the 17th Illinois. He led the 8th Illinois Cavalry during the Peninsula Campaign, seeing action at the Battle of Williamsburg and in the Seven Days Battles.