Conventional submarines produced to date can be more easily detected and exposed to attacks due to their visible, infrared, and radar signatures. Diesel-electric submarines need to come to a close surface at certain time intervals to charge their batteries and power their diesel generators with snorting systems. This situation causes submarines to face threats from land, sea, and air war elements. In order to reduce these threats, it is clear that there is a need for an innovative system in which the need for submarines to the surface is minimized and the timing of emergence is more flexible. To ensure this situation, air-independent propulsion systems have come to the fore from past to present and have gained more and more strategic importance. These air-independent systems significantly improve silent underwater time, and maneuverability and greatly contribute to maintaining the submarine's military stealth strategy. In this context, in this study, six different power system alternatives used as air-independent propulsion (AIP) submarine systems were evaluated, their advantages and disadvantages were compared, and alternatives were sorted by five experts in terms of nine important technical and economic criteria with the fuzzy VIKOR method. It has been seen that the propulsion power with the fuel cell system comes to the fore. The choice of a high power density fuel cell system for a submarine AIP system can allow for superior underwater range and durability and a minimal rate of instability and thermal signature than would be achievable from any heat engine. This will greatly expand the strategic advantage of AIP submarines. In this respect, this article can be a guide in understanding the critical technical features of submarines and in deciding between alternatives in submarine system selection.