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The Clarets, relegated from the Premier League last season, have won only one of their 12 league games under former Genk boss Hayen, 46, who was appointed in July as a replacement for Scott Parker.
A brief statement on the club’s official website read: “Burnley Football Club has dismissed head coach Nicky Hayen with immediate effect.
“The Board has taken the decision following a disappointing start to the Championship season.”
The Clarets’ loss at Lincoln was their sixth in the league this season and has left them third from bottom in the table, three points from safety.
Belgian Hayen was named as Parker’s successor after Burnley had failed to land Wales boss Craig Bellamy and former Wolves manager Rob Edwards.
Hayen had earlier said in his post-match press conference, before news of his dismissal emerged: “It’s frustrating for everyone, especially the fans. I want to apologise to them, but I know it doesn’t matter because it’s another hard defeat for them and I can understand their criticism.
“We haven’t got the results. I will keep on working hard as long as I have the chance. But there will be a day if it carries on like this that it stops.
“I don’t know (if I will still be in charge). I know it’s a really tough defeat and something to think about for the board.”
Lincoln boss Tom Shaw said it was a day to savour after his side’s impressive win at Sincil Bank.
The Imps came from behind after Andreas Hountondji’s opener. From that moment on it was one-way traffic.
Mikkel Ladefoged marked his first league start for the club with a brace whilst Ben House and Dom Jefferies got the other goals in a deadly display. George Wickens played a late part as he kept out Marcus Edwards’ penalty.
Shaw, whose side ended their four-game winless run in style, said: “I’m delighted. I’m delighted for a few groups of people – the staff and the players for the work ethic and what goes on behind the scenes that you really don’t see.
“Probably more importantly than anyone is the supporters. We felt we owed them one for the West Ham experience. It’s a game we wish we could have back. We owed them something.
“We felt we were a little bit short points wise for our performances here. So we knew this was a big day and a big opportunity.
“We got our reward of Lincoln City beating Burnley 4-1 in a league game.
“You’ve got to remember the journey and all the people that helped us get here.”