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The Northern Irish defender attended the ceremony with Imps manager and current League Championship Two Manager of the Month Keith Alexander.
"It was a great experience, but was totally unexpected," said Morgan who signed for City from Preston in 2001 and has since made 148 appearances in a Lincoln shirt.
"There were some very good footballers in the nominated group and I am honoured to win it. I think awards like this are just a sign of the success we are having at Lincoln City at the moment and have had over the last couple of years. The gaffer was with me last night and he was over the moon and very happy for me. However just like his recent award, it comes because of the hard work put in by the whole side."
City are one of the in form teams in League Two at the moment having won four league games in a row scoring ten times in those four games.
"Awards like this are down to the fact the success of the team is making people look at us."
Imps chairman Rob Bradley revealed he was delighted the club was finally recieving some recognition for the excellent work put in by all over the last two and a half seasons.
"It is tremendous to see Paul scoop the footballer of the year award and everyone associated with the club is very proud of him," said Bradley.
"He quietly goes about his business and is hardly ever recognised, but he is one of the best defenders we have had at the club in the last 30 years. He rarely gets man of the match because supporters expect him to play like that every week. It is good people now realise what he has done for Lincoln."
Morgans award adds to speculation he could find himself pulling on the green jersey of Northern Ireland very soon. Indeed if Lawrie Sanzhez is to travl across the country to watch Andy Kirk in action at Boston, it'd be hard not to contemplate popping over to Sincil Bank to witness a player every inch as good at stopping goals as Kirk is netting them.