Brownlee was focusing on long-distance events this year and won on his debut in the Ironman 70.3 series at the North American Championships in May.
The 29-year-old also won the World Triathlon Series event in Leeds in June.
"It has been a tough decision, but suffering from an acute flare I am left with little option," said Brownlee.
In a post on social media, he added: "Unfortunately it will take me away from competing for the rest of the year but I hope it will enable me to continue doing what I love for many years to come."
Victory in Utah three months ago had earned Brownlee - a gold medallist at the London 2012 and Rio 2016 Olympics - a spot at September's Ironman 70.3 World Championship.
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British double Olympic champion Alistair Brownlee will not compete again in 2017 after having hip surgery.