The present invention relates to a fuel cell cooling system for a vehicle comprising: a cooling water circulating loop formed to cool a fuel cell stack where a plurality of fuel cells are stacked. The cooling water circulating loop includes: a plurality of cooling water introducing ports through which cooling water passing through the stack is introduced; a plurality of cooling water discharging ports corresponding to the plurality of cooling water introducing ports and through which the cooling water which has passed through the stack is discharged; and a plurality of cooling water channels connecting the plurality of cooling introducing ports and the plurality of cooling water discharging ports. Notably, cooling water flows in different directions in the plurality of cooling water channels.