Recent improvements in diagnostic modalities are increasing the frequency of detection of small-sized branch duct intraductal papillary mucinous neoplasms (BD-IPMNs). International consensus guidelines for IPMN recommend surveillance without immediate resection for small-sized (<3 cm) BD-IPMNs without malignant features on imaging. Our patient is the first to have undergone resection of a small-sized BD-IPMN containing invasive cancer, but without malignant features on imaging. We herein report a case involving a 70-year-old man with a small cystic lesion in the pancreas head detected by health screening ultrasonography. Detailed examination revealed that the cystic lesion was a BD-IPMN measuring about 2 cm, with no malignant features. However, cytological examination of the pancreatic juice showed atypical cells with high-grade dysplasia storing intracytoplasmic mucin, indicating malignant BD-IPMN. Pathological examination of the resected specimen showed a BD-IPMN measuring 16 mm with an associated invasive carcinoma that invaded the pancreatic parenchyma over a distance of 11 mm. In this patient, invasive cancer was present within a small BD-IPMN with no high-risk stigmata on imaging. Cytological examination of the pancreatic juice allowed for the detection of pancreatic cancer in such a small-sized IPMN. Although routine endoscopic retrograde cholangiopancreatography (ERCP) with cytology is not recommended in all patients with BD-IPMNs, ERCP may contribute to the detection of small pancreatic cancers in select cases. Accumulation of cases of pancreatic cancer within small BD-IPMNs may help establish the indications for ERCP with cytological examination for the purpose of early detection of small pancreatic cancer.