Surgical site infections (SSIs) following a pancreaticoduodenectomy have been a significant cause of morbidity and even mortality. A modified sequence of the Whipple procedure, using the COMBILAST technique, may reduce SSIs and the patient’s hospital stay. This prospective cohort study included 42 patients undergoing Whipple’s pancreaticoduodenectomy for a periampullary malignancy. The modified sequence pancreaticoduodenectomy technique, COMBILAST, was used to estimate the incidence of SSI and explore other advantages. Of the 42 patients, seven (16.7%) developed superficial SSIs, and two patients (4.8%) had an additional deep SSI. Positive intraoperative bile culture had the strongest association with SSI (OR: 20.25, 95% CI: 2.12, 193.91). The mean operative duration was 391.28 ± 67.86 min, and the mean blood loss was 705 ± 172 mL. A total of fourteen (33.3%) patients had a Clavien–Dindo grade of III or higher. Three (7.1%) patients died of septicemia. The average length of a hospital stay was 13.00 ± 5.92 days. A modified sequence of the Whipple procedure, using the COMBILAST technique, seems promising in reducing SSIs and the patient’s hospital stay. As the approach is only a modification of the operative sequence, it does not compromise the oncological safety of the patient. Moreover, it has an added surgical advantage in reducing the chance of injury to the aberrant or accessory right hepatic artery.