The star player from Thornhill, Ont., who had foot surgery in May, said he was hurting "all over" by the end of his 5-7, 7-5, 7-6 (3), 6-3 third-round defeat.
The seventh-seeded Raonic was clearly suffering as the match went on. He called his foot the "instigator," but said he was feeling pain in many places.
"I'm just dealing with a lot of things," said the 24-year-old. "I still have some discomfort in my feet, so compensations and stuff like this just make any pain pretty much come up. The more I got through the match the more difficult it was."
"First, ankle, then the hip, and then the back," he added. "Then when those things aren't working, you just put too much pressure on your shoulder, and then your shoulder hurts."
The Canadian said he had been expecting to have these issues during his recovery but it just became too much to overcome against Kyrgios, the 20-year-old rising star who stunned star Spaniard Rafael Nadal here last year.
"It's disappointing," said Raonic. "I wanted this tournament to last longer, but it is what it is."
Raonic said even his reliable, blistering serve abandoned him.
"Oh, it wasn't even there at the beginning of the match," he said. "It wasn't there. It's just things I was dealing with from the start of the day from even the previous match, and I tried (to) make the most of it. That's it. I had what I had, and I put it all out there."
Kyrgios, who lost to Raonic in the 2014 quarter-finals, served 34 aces and hit flashy winners from all over the court to reach the round of 16.
"I don't fear anyone," the 26th-seeded Kyrgios said. "I definitely feel I'm playing better tennis than last year."
The battle on Court 2 featured two of the young stars of the game and two of the biggest servers in tennis. While Raonic was stolid and businesslike, Kyrgios was as flamboyant and expressive as ever.
He went for spectacular winners, bantered with the crowd, pumped his fists and shouted. He hit three aces in a row in two different games. He hit second serves at 200 km/h. He waved his arms in the middle of a point that he lost. He hit a between-the-legs shot from close to the net that went long.
Kyrgios received a code violation in the second set after slamming his racket to the ground so hard it bounced over the back wall into the crowd. A male fan caught it and handed it back to him.
"I don't want to hurt anyone," Kyrgios said. "It was a good catch by the fan anyway."
Raonic said he barely noticed Kyrgios's antics.
"I had too many of my own things to be concerned about," he said. "That was a distraction enough on its own."
Kyrgios came out during the second set sporting a Wimbledon headband in the club's official green and purple colours — only to be told that it was too colourful for the tournament's dress code. So he turned the headband inside out and wore it that way for the rest of the match.
"They told me to turn it around, so I turned it around," Krygios said.
The match turned in Kyrgios' favour when he broke for a 6-5 lead in the second set. Raonic was at the net and poised for a forehand volley but let the ball go and watched Kyrgios' forehand pass fall in for a winner. Kyrgios hit three aces in a row in the next game to close out the set.
Raonic finished with 18 aces, but broke only once out of seven chances. Raonic had 62 total winners, one more than Kyrgios, but the Australian had only 13 unforced errors, compared to 21 for the Canadian.
Kyrgios next faces Richard Gasquet, who dismantled No. 11 Grigor Dimitrov 6-3, 6-4, 6-4 on Friday.
Raonic said he plans to get his foot checked by his doctor but plans to play in Davis Cup later this month in Belgium.
Vancouver's Vasek Pospisil is the lone Canadian left in the singles draw. He plays Britain's James Ward in the third round on Saturday.
— With files from The Associated Press
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