It depends if the boy (he) is referring to himself or if he is talking to another person. Also if it's in past or present. Here is how I would write it. VVVV
Referring to another person: He said, "You had permission to come at any time."
Referring to himself: He said, "I had permission to come at any time."
(Or possibly He said, "You had given me permission to come at any time.")