Pharmacists are very well compensated for the services they provide. The average annual pharmacist salary is $116,500. The bottom 10% of pharmacist make less than $89,000 while the top 10% of pharmacist make well above $147,350.California holds the highest level of employment for this profession. quick glance at the pharmacist salary trend over the last 10 years is very encouraging. In 2004, the average salary of a pharmacist reached $84,000 per year. In 2008, their annual salary jumped to $104,000.