The astonishing scene was captured on video by a couple of fans as McIlroy prepared to tee off at 8am in the marquee group in the $8 million Rolex Series event alongside world No 1 Jon Rahm and third-ranked Justin Thomas.
McIlroy said after his round that he’d been “surprised” by the incident but reckoned it had been “handled efficiently”.
The 10th tee at the East Lothian venue is about 30 yards away from the closest point fans are allowed and it is unclear how the individual managed to get as close as he did to the players.
In a video posted on Twitter but later taken down, McIlroy was seen chatting to his caddie Harry Diamond and Rahm when the man appears on the tee.
Taking the trio by surprise, he grabbed the head cover off McIlroy’s driver then took an iron out of the bag before moving across to the other side of the tee.
McIlroy’s reaction was a double take, with the world No 11 looking on incredulously as the man looked as though he was going to hit the head cover with the club.
An onlooker told The Scotsman: “When someone told him that he couldn’t do that, he replied by saying ‘why not?
“At that point, the security people assigned to following the group moved in and took him away.”
Kilspindie member David Wilson, who posted another video of what happened, described the man as “some random”.
He added: “He was quickly dealt with. The players laughed it off, saying they knew he wasn’t a golfer when they saw his grip!”
McIlroy, who was in danger of missing the cut after completing his opening 36 holes in one-under, spoke briefly about the incident afterwards.
"It was a surprise, yes, but it was handled efficiently and everything's okay," said the Northern Irishman. "I had no idea who he was."
He agreed there was a serious aspect to security breaches of that sort, but added: "Again, it was handled quickly, and that was an end to it."
A spokesperson for the European Tour said: “At approximately 8am on Friday morning, a spectator entered the tenth tee area."He was quickly escorted from the tee by security personnel and the matter is now in the hands of Police Scotland.”
A spokesperson for Police Scotland added: "Officers were alerted to a man causing a disturbance within the grounds of the Renaissance Club in East Lothian, around 8am on Friday 9 July.
"The 35-year-old man has been taken to the Royal Infirmary of Edinburgh and enquiries are ongoing.”
The event is the first in Scotland to be held with fans since October 2019, with a strictly-limited attendance, believed to around 4,000 people per day – being allowed on site.
The likes of McIlroy and Rahm are assigned security people at European Tour events and incidents are few and far between.
“It was early and there are some areas people can try to exploit,” said Rahm after posting the clubhouse target of 11-under after adding a 65 to his opening 66.
“For the most part, the Scottish people love the game of golf. They would never try to do things like that.
“Me and Rory and Adam were just looking. Like ‘what is going on?’ After a little bit, when he walked back and they were taking him out you could smell the reason why it happened.
“Let me put it this way: you could smell the reason why he did what he did. He was clearly not sober. I’m going to say it was vodka. I’m no expert, but he had a long night for sure.
He probably thought it was a fun idea. And, to be fair, it was quite funny.”
Asked if he’d felt threatened, Rahm replied: “No. Me and Rory didn’t say anything. He was holding a 6 iron and I didn’t want to get hurt.”
The Spaniard described the security as “good”, adding: “These things can happen. He had good timing. He walked in very confidently.
“We were all thinking, ‘maybe he is supposed to be doing this.’ We didn’t know. We thought he was from television or a magazine and was going to take a picture.
“Then we realised that was not the case when he started to tee-off with the head cover.
“But, for the most part, Rory and I both thought it was a prank or someone who was supposed to be there.
“We had three or four security guys with us. Two walk with us. And they did what they have to do. It was just someone who took advantage.”
The 10th tee at The Renaissance Club sits close to a boundary wall with Muirfield.
“I’m still not sure where he came from,” said Rahm. “There is a fence there, maybe he came from there. I don’t know.”