We experienced a rare case of isolated lateral lymph node (LLN) recurrence after laparoscopic intersphincteric resection with total mesorectal excision for T1 lower rectal cancer that was successfully treated using LLN dissection with en bloc resection of the left superior vesical artery, the left ovary and the left obturator nerve, artery and vein. There are no guidelines for treating patients with isolated LLN recurrence because isolated LLN recurrence is rare, especially in patients with T1 rectal cancer. However, in patients with pT1N0 lower rectal cancer, follow-up examinations of the pelvis should be performed periodically. Patients with isolated LLN recurrence treated with surgery might have good long-term prognoses. Therefore, for such patients, surgical resection should be considered as a curative treatment only.