The impact of maltodextrin (10%) in combination with trehalose or glycerol at different levels (2.5% and 5%) and their mixture on the stability of freeze-dried pepsin from skipjack tuna stomach was studied. Addition of 5% trehalose and 10% maltodextrin yielded the powder (TPP-T5) with highest relative pepsin activity (p < 0.05). TPP-T5 had different shapes and sizes, with mean particle size of 65.42 ± 57.60 μm, poly-dispersity index of 0.474, and zeta potential of −19.95. It had bulk density of 0.53 kg m−3 and possessed fair flowability. The wetting time for TPP-T5 was 16.36 ± 0.73 min, and solubility was 93.58%. TPP-T5 stored at room temperature under different relative humidities could maintain proteolytic activity up to 4 weeks. Commercial porcine pepsin (CP) and crude tuna pepsinogen had molecular weights of 35.2 and 43.3 kDa, respectively, when analyzed using gel filtration (Sephadex G-50) and SDS-PAGE. Tuna pepsin had comparable hydrolysis toward threadfin bream muscle protein, whey protein isolate, and kidney bean protein isolate to commercial pepsin, especially at a higher level (15 units/g protein). Digested proteins contained peptides with varying molecular weights as determined by MALDI-TOF. Therefore, pepsin from skipjack tuna stomach could replace commercial porcine pepsin and was beneficial supplement for patients with maldigestion, particularly the elderly.