"Ro-49" set out from Kure on 1 January 1945 to begin her second war patrol, again in the Philippine Sea east of the Philippines. On 4 January 1945, she received new orders to patrol in the South China Sea west of Luzon. U.S. forces entered Lingayen Gulf and U.S. forces began their invasion of Luzon on 9 January 1945. "Ro-49" was in the South China Sea west-northwest of Iba on Luzon on 12 January 1945 when she sighted two escort aircraft carriers and three battleships with a strong escort. She attacked and her commanding officer reported that she sank what he described as an ""Idaho"-class" battleship, but her claim of hitting a battleship was disproven after World War II. On 21 January 1945 he received an order to return to Kure, which she reached on 1 February 1945. She moved to Saeki on 16 March 1945.