The school opened in September, despite the refusal of permission. Later in the same month, Bedford Borough Council withdrew a notice that could have forced pupils to move out.
In a decision letter issued last week, Pickles agreed with his inspector that the appeal should be allowed and permission granted.
The council refused the application on the basis that it would generate traffic and pick-up and drop-off activity that would give rise to increased danger and inconvenience to users of the highway and nearby premises and adversely affect the flow of traffic on a primary route into the town centre.
But Pickles agreed with his inspector’s conclusion that the proposed use "would not result in a significant generation of pick-up and drop-off activity and thus would not adversely affect the free flow of traffic on a primary route into the town centre or be detrimental to highway safety".
Pickles concluded that the appeal proposal "accords with the development plan and national policy and that there are no material considerations of sufficient weight to justify going against that".
The decision letter said that Pickles is satisfied that the proposal "would not have any worse effect on the gyratory system than the current arrangements and could have a positive overall effect".
Ian Pryce, chair of Bedford Free School governors, said: "Our advice has been clear throughout that planning consent would be achieved. While we accept the borough’s planning decision stemmed from genuine concern by members, it is a shame that it lengthened the process, and unsettled parents and pupils at an important time."
The decision letter (DCS Number 100-079-772) can be purchased from DCS Ltd (tel) 01452 835820 or email email@example.com