Is it permissible for an employee to keep the price difference after purchasing a medicine at a lower price from the pharmacy where he works and selling it to the customer at market price?

The employee in the pharmacy is a private employee, and his benefits during working hours belong to the pharmacy owner. He is an agent for the owner in sales. Therefore, the employee does not own the right to sell anything to himself unless with the permission of the pharmacy owner, because agency necessitates seeking the best price, which is not achieved when selling to oneself. Hence, the difference you obtained from the medicine is the right of the pharmacy owner, and it is not permissible for you to take it except with his permission.