Abstract Background Clinical Pharmacist Practitioners are advanced practicing pharmacists in North Carolina that provide disease-specific management. The purpose of this retrospective cohort study was to compare the efficacy and charges from referrals to a Clinical Pharmacist Practitioner by the primary care provider, to those managed by a primary care provider alone. Methods Patients were separated into cohorts depending if they had at least two appointments with a Clinical Pharmacist Practitioner from November 2008 to November 2011. A primary care provider saw all patients at least twice during the study period. Cohorts were then matched by age, gender, and disease states. Medicare billed data was evaluated from outpatient visits related to hypertension, diabetes mellitus, and peripheral neuropathy, as well as emergency department visits and inpatient admissions. Cost of medications was estimated using 2009 AWP data corresponding to medication histories within the electronic medical record. Efficacy was defined as ability to reach disease state goal determined using national guidelines and reduction in pain score. Efficacy was analyzed by difference-in-differences test and all other numerical data tested by paired t-tests. Results The Clinical Pharmacist Practitioners cohort experienced more outpatient visits (1338 vs. 858, p < 0.001), fewer emergency department visits (115 vs. 190, p < 0.05), and similar inpatient admissions (88 vs. 117, p > 0.05) than the primary care providers cohort, respectively. The Clinical Pharmacist Practitioners cohort showed changes in charges of +22.6 % for outpatient visits, −45.5 % emergency department visits, and −13.2 % inpatient admissions relative to the primary care provider cohort. There was no difference in average daily medication cost (Clinical Pharmacist Practitioners $38.52 vs. primary care providers $38.23, p = 0.97) or achievement of disease state goals. Conclusion APPLE-NC demonstrated that through referrals, Clinical Pharmacist Practitioners provide services comparable in charges and efficacy to primary care providers. Consequently, the current increased need for primary care practitioners can be met in part by increasing the utilization of advanced practice pharmacists for chronic disease management. Trial registration This does not apply for this retrospective cohort study.