Two types of fuel cell systems using NaBH4 aqueous solution as a fuel are possible: the hydrogen/air proton exchange membrane fuel cell (PEMFC) which uses onsite H2 generated via the NaBH4 hydrolysis reaction (B-PEMFC) at the anode and the direct borohydride fuel cell (DBFC) system which directly uses NaBH4 aqueous solution at the anode and air at the cathode. Recently, research on these two types of fuel cells has begun to attract interest due to the various benefits of this liquid fuel for fuel cell systems for portable applications. It might therefore be relevant at this stage to evaluate the relative competitiveness of the two fuel cells. Considering their current technologies and the high price of NaBH4, this paper evaluated and analyzed the factors influencing the relative favorability of each type of fuel cell. Their relative competitiveness was strongly dependent on the extent of the NaBH4 crossover. When considering the crossover in DBFC systems, the total costs of the B-PEMFC system were the most competitive among the fuel cell systems. On the other hand, if the crossover problem were to be completely overcome, the total cost of the DBFC system generating six electrons (6e-DBFC) would be very similar to that of the B-PEMFC system. The DBFC system generating eight electrons (8e-DBFC) became even more competitive if the problem of crossover can be overcome. However, in this case, the volume of NaBH4 aqueous solution consumed by the DBFC was larger than that consumed by the B-PEMFC.