Reid was a target for the Gabba crowd last Sunday and playfully flashed his middle finger to Lions fans after one of them had offered him a packet of tissues.
The 19-year-old escaped a fine from the AFL's match review officer, but league officials stepped in and asked the Eagles to explain the marquee midfielder's actions.
Having obtained further context around the incident, the AFL on Wednesday charged Reid with misconduct.
"After requesting a please explain and reviewing Reid's submission, the AFL determined his actions during Sunday's game warranted a financial sanction," the league said in a statement.
Reid, the No.1 draft pick in 2023, has faced plenty of criticism over his actions during West Coast's defeats to Gold Coast and Brisbane at the start of his second season.
He struggled in the Eagles' home loss to the Suns and while he was more involved against the Lions, he also gave away seven free kicks.
Reid had an altercation with Brisbane veteran Dayne Zorko and showed his middle finger to the crowd during the final quarter after a tangle with Oscar McInerney near the boundary.
The criticism has come despite post-match pleas from first-year Eagles coach Andrew McQualter.
"There's a fair bit of commentary about Harley all the time, so last week was not necessarily different," McQualter said on Sunday.
"We try and bash the theatre out of this game, don't we?Â
"He's just having a bit of fun and sometimes that's good for the game, I think."
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