Despite optimistic preseason predictions, Tulane suffered its first and only losing season of Shaughnessy's tenure in 1926. He was considered for the head job at Northwestern in February 1927 after Clarence Spears turned it down. Shaughnessy later received similar offers from Louisiana State and Wisconsin. On April 8, 1927, he tendered his resignation without a publicly stated reason and was subsequently released from his contract. Tulane replaced him with former assistant Bernie Bierman. "The Milwaukee Journal" credited Shaughnessy with building a formidable team at Tulane, and noted that he increased revenue and improved facilities, while he used the available players and did not pay them "a nickel". At the end of his tenure, Shaughnessy held a record of 59–28–7, and as of 2010, he continues to hold the record for the most wins of any Tulane football coach. He also coached the basketball team for three seasons between 1915 and 1918 and amassed a 27–15 record.