Klonipin generally stays in your system for 36 hours to three days hours per 1mg. The rate that your metabolism works is a major factor. Slower metabolisms will cause the drug to stay in your system longer. The higher the dosage you are on, the longer it will be in your system, with four days being the general maximum for a single dose. If you take klonipin regularly, it could take up to two weeks to completely leave your system.