In Japan, based on the Ministry of Health, Labour and Welfare’s “Pharmacy Vision for Patients” (2015), there has been a growing need to shift from “drug-centered, physical work” to “patient-centered, interpersonal work.” Medication counseling is one of the most important tasks of pharmacists. In the present study, we focused on the questions asked by patients during medication counseling, and statistically analyzed the content of the questions and the patient attributes obtained from the patient medication profile. The study was conducted from 2018 to 2019 on patients who visited two pharmacies. Data from a total of 3,300 patients was collected, of which 859 asked questions during medication counseling, accounting for about 26% of the total. Attributes that significantly influenced the asking of questions included gender, new prescriptions, and who was being instructed, especially for women and parents of infants. In terms of topic, questions about the duration and timing of taking the medication and about the medication itself were common in all departments. In terms of medication effects, there were many questions about topical and central nervous system medications, but there were also questions about non-medication matters such as tests. When providing medication counseling, it is expected that pharmacists will actively provide instructions to resolve patients’ questions based on the characteristics of each pharmacy and on patient demographics, as well as improve the quality of interpersonal services according to the patient’s background.