Our CVS Pharmacy Managers in California make an on average between $106K and $150K per year. Our Store Managers make on average $53K - $63K. Store managers are responsible for the operation of the entire store, while pharmacy managers manage only the pharmacy operations.pharmacy managers have more specialized skills and educations requirements. Recently, some store managers have been complaining about the unequal pay they receive in comparison to pharmacy managers. They claim that CVS should administer equity in pay to all their managers (not including assistant managers). Should pay be equitable across all managers within the same store/company regardless of education requirements and specialized skills sets? PRO: Yes, pay equality for all managers within the same company store. Equal pay for equal work. CON: No, educational background and specialty of skill sets can increase the value of the position and employee to the company