Rooney was jeered by frustrated England fans after the Manchester United star capped a lacklustre performance with a wayward shot in the closing stages of his country's 2-0 win over Malta at Wembley on Saturday.
The England captain had already endured a difficult season, with United manager Jose Mourinho dropping him recently, but the taunts that greeted his underwhelming effort against minnows Malta were a new low.
Henderson is confident Rooney will be able to ignore the boos because he has become accustomed to dealing with scrutiny and criticism throughout his career.
"Wayne's experienced enough to know he has to concentrate on his football. I think he's had criticism for most of his career, like many players have," Henderson said.
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"He deals with it very well. He's our captain and our leader. He's a fantastic player for Manchester United and England. The Liverpool midfielder continued, "I didn't really hear any boos, but we have to deal with it as professional footballers. There is going to be criticism along the way."
Rooney wasn't alone in having to deal with jeers during the World Cup qualifier as there were boos for the whole team following a disjointed second half.
Henderson admitted the fans' criticism was inevitable after England's embarrassing Euro 2016 exit against lowly Iceland.
"I said during the week the fans had a right to criticise after the way we went out of the Euros. Not only the Euros but in the World Cup as well. We've got to take the criticism and we deserve it. But I feel as though they know we are a good team and want us to do well. It's up to us to put in good performances and win games," the Liverpool captain said
Rooney had spent his entire career as a striker until last season when former United boss Louis van Gaal used him in midfield with limited success.
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Mourinho is adamant the 30-year-old's best position is up front, but England interim manager Gareth Southgate disagrees and deployed Rooney in a deep-lying midfield role on Saturday.
Rooney looked a fish out of water for long spells and Henderson, who played alongside him in midfield, conceded their partnership still needs work.
"I felt he had a good performance. He got on the ball and broke it up at times," the English international said. "It was just making sure that we were communicating and making we weren't both getting ahead of the ball and leaving gaps in the middle. "I felt we had that balance most of the time but there were a couple of occasions when it could have been better, so we will look back at that and that's an area we need to improve on," the 26-year-old continued.
Southgate refused to take the bait when asked if Rooney's display showed Mourinho was right.
"Look, Jose will have his opinion on what's right for his team. I have to pick a team to get a result today. I don't see any point in getting drawn into that," he said.
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