The high-temperature short-time (HTST, 72 °C, 15 s) pasteurization of human milk (HM) has been proposed as an alternative to the Holder method (HoP, 62.5 °C, 30 min), to increase the preservation of bioactive compounds. We have investigated the impact of HTST and HoP pasteurization on the gastrointestinal kinetics of human milk, using a dynamic in vitro system in a preterm newborn model. An increased protein aggregation on the surface of fat globules following pasteurization, albeit to a lesser extent in HTST than in HoP, was observed. Despite relevant differences in the undigested milk samples, both pasteurization methods led to similar proteolytic patterns, while raw HM presented a higher native lactoferrin content throughout digestion. The slightly decreased amino acid release following HoP, with respect to HTST and raw HM, indicated that peptidomic analysis, which is currently underway, might provide interesting insights on the differential digestive kinetics of differently pasteurized HM.