The Gillingham boss scooped the honour having led the Kent club to the League Two title this season in his first campaign at the helm.
"I am thrilled, honoured, shocked and surprised to be named the Manager of the Year for League Two," Allen told the club's official website.
"It was only a year ago I was looking for different career options and was hoping talkSPORT or Sky Sports would give me an opportunity, or maybe a place on the after-dinner speaking circuit, after Barnet had told me I was not going to be offered a contract.
"I still have to pinch myself that all this has happened so quickly."
