What is the context of the phrase? If it is in this type of situation:

"I think it should be this."
"Whatever you say."

Then it usually means the person does not wish to argue about it, or doesn't have a preference.

If I were to be arranging a meeting with a friend, and they said, "I think we should meet in the afternoon," to which I responded "Whatever you say." Then it means I don't have a preference.