The Gilbert and Marshall Islands campaign began on 20 November 1943 with the U.S. invasion of Tarawa and of Makin in the Gilbert Islands. On 21 November 1943, "I-39" received orders to proceed to Tarawa along with the submarines , , , and . With a Yokosuka E14Y1 (Allied reporting name "Glen") floatplane aboard, she got underway from Truk on her second war patrol that day, with an assigned patrol area southwest of Tarawa. She reported on 24 November 1943 that she was approaching her patrol area, and on 25 November — the same day she was reassigned to Submarine Division 2 in Submarine Squadron 1 — she reported that she had arrived in her patrol area. The Japanese never heard from her again.