The medication experience is an individual’s subjective experience of taking a medication in daily life and can be at the root of drug therapy problems. It is recommended that the patient-centered approach to comprehensive medication management (CMM) starts with an understanding of the patient’s medication experience. This study aims to develop a medication experience documentation tool for use in CMM services, and to understand the usefulness and challenges of using the tool in practice. The tool was developed based on previous research on patients’ medication experiences. It was tested in two rounds by ten CMM pharmacists utilizing the tool as they provided care to patients. Focus groups were conducted to revise the tool after each round and to understand pharmacists’ experiences. The tool was tested for 15 weeks in 407 patient encounters. There was at least one medication experience documented in the electronic medical record 62% of the time. Pharmacists found the tool helpful in raising awareness of the medication experience and motivational interviewing strategies, planning for follow-up visits, as a teaching tool, and making pharmacists realize the fluidity of the medication experience. The tool offered pharmacists a better way to recognize and address medication experiences affecting medication taking behaviors.