The aviation sector in the Philippines offers various local and commercial airlines, with mainline, regional, and charter airlines operating in different sectors. This study discussed the research opportunity on determining the airline preferences among Filipinos in association with the SERVQUAL model and Rational Choice Theory. The variables conceptualized in relation to Airline Preferences show the independent variables derived from the Rational Choice theory, namely Customer Lifestyle, Flight Comfort, and Flight (airline) Safety. Partial Least Square - Structural Equation Modelling (PLS-SEM) was used to assess the structural importance of independent variables in relation to dependent variables. 625 Filipinos were gathered to assess these factors, with the respondents being Filipino citizens, at least 18 years old, and having traveled through air transportation at least once in their lifetime. Having 622 valid responses out of 625, results showed that in the SERVQUAL model, Customer Satisfaction is the most significant factor in Filipinos’ perceived airline preference, while for the Rational Choice Theory, its was found that Customer Lifestyle had the strongest influence on Resource Allocation. Given these, it was recommended that airlines should prioritize improving their overall service quality and focus on aligning their services and marketing strategies to different lifestyle preferences.