AFL CEO Gillon McLachlan says he was "agitated" by the decision that overturned a two-match suspension for Patrick Cripps that ultimately paved the way for Carlton's superstar to secure his first Brownlow Medal.

Cripps was offered a two-match ban by the Match Review Officer following a round 21 collision with Callum Ah Chee that left the Brisbane utility concussed and sidelined for two weeks.

He went to the Tribunal, where the decision was upheld, before Carlton rolled the dice one final time at the AFL Appeals Board.

It was there that the initial suspension was overturned due to a procedural error in the initial hearing.

In an interview given to the AFL Record Grand Final edition prior to Sunday night's Brownlow count, McLachlan said it made "no sense" to him that Cripps got off.

“People are aware I was very agitated by that decision,” McLachlan said.

“It made no sense to me in any way, and it is frustrating to have a legal view about due process or procedural fairness - a complete nonsense - really affect a clear mandate to protect the head.

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“We confused our supporters and set ourselves back and that really frustrates me.

“When you can have something that is so important, which is protecting the head, and a clear statement from the MRO and backed up by the Tribunal, and then the player getting off because of a legal technicality and nobody really understanding what the hell happened, I find that challenging."

On Monday, McLachlan clarified his comments, making pains to separate his criticism of the decision from Cripps' win.

"I'm not sure I can remember a more worthy and certainly popular winner than Patrick Cripps. There is not one part of that (appeal), that in my mind that diminishes that win last night," McLachlan said. 

"He is tough and brave, if you look at that game in round 23 against Collingwood, I haven't seen a player want to get the ball, to run through people, to cast them aside – he is incredibly worthy Brownlow Medal winner. Anything related to that appeal process is separate and in no way is related to his worthiness as a Brownlow medal winner.

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"You know what I thought of the decision, I thought it was confusing at best. That was a comment on the Appeals Board's decision, and that decision, nothing to do with Patrick Cripps. He is entirely eligible, he was cleared by the Appeals Board, and I think he's a fabulous footballer, person and incredibly worthy Brownlow winner."

Cripps was available to play Carlton's final two matches, with a herculean round 23 performance against Collingwood enough to earn him three votes and vault him ahead of Lachie Neale.

Cripps finished with 29 votes, one clear of Neale, with Gold Coast's Touk Miller a further vote back on 27.

McLachlan, who will finish his role with the AFL in coming months, said he'd like to see some change.

“I have asked the guys to review the system and we will see where that lands," he said.