up to 2 days maximum. from the first day you don't take a pill, do not count on it to prevent pregnancy. If you have unprotected intercourse after you stop taking the pill, go to your doctor or local clinic and get the morning after pill within 48 hours. Hello.Birth control remains in your system for a total of three months once you stop taking it. However when you miss one pill this does put you at risk of pregnancy.sually around 3 months. Pills are out of your system pretty much immediately. That is why they say if you skip two pills, you have to use a backup birth control method for a week. Other things like shots, patches, etc. can take a few months.