At the beginning of the War of the Pacific, Lynch was a Naval Commander. He asked for a position in the navy, but was refused due to the opposition of his fellow officers. He retaliated by asking for a position in the Army, but instead was named as Commander General of Transports, where he was able to show his great abilities as an organizer. In early September 1880, he led a raid against northern Peru to gather ransom payments from business and sugar plantation owners, that has become known as the "Lynch Expedition".