Is there any side effect of pepcide (famotidine) for 5 week old? my concern is on long run and stomach acids impact of the dose (if any)?

Probably not: Not clear what you would be treating a 5 week old with Pepcid (famotidine) for without a physician's input? In any case if you give a low 5 -10 mg dose maybe some sedation would be expected but i don't think that i would use Pepcid (famotidine) for long though. See your doctor this might be an intolerance to formula or even breast milk sometimes.