In 1862, while preaching in Montrose, Pennsylvania, Van Valkenburg received a summons to arms, as it was believed that the Confederate army was planning to attack the city of Harrisburg. Van Valkenburg quickly raised a company of one hundred and eight men, who elected him as their captain. This company served at the front, but were returned home after the Battle of Antietam and relegated to a reserve force. The company was eventually called out again and were stationed in Carlisle, Pennsylvania the night before the Battle of Gettysburg. After this Van Valkenburg volunteered to become a chaplain of the pioneer corps, where he accompanied General Sherman on his march through Georgia. Van Valkenburg became seriously ill and was hospitalized in Atlanta for a period of two months.