The copay will be the same if certain conditions are true.
(1) we are taking about a fixed price copay and not a percentage copay. If it is the latter, then the price you pay will be a function of the retail price of the drug. This less favorable copay is sometimes used when your doctor requests that the prescription be filled with a name brand instead of a generic.
(2) both pharmacies are in network and in the same tier. I believe ExpressScripts has in network and in network preferred with better price at the latter. Also some insurance companies own pharmacies and your plan description will indicate a different co-pay for them.
(3) we are comparing the same prescription. There was a comment on another answer about the mail order pharmacy option that is often offered for 90 day scripts. A 90 day script is different than a 30 day script. There are often bulk discounts associated since you are sent an entire bottle (no need to count out pills).
So in summary if you are considering a 30 day fill at two pharmacies that are both in network at the same tier and three drug is covered with a flat copay, then the copay will be the same at both.