Fans noticed that while XS, small and medium sizes cost $40 (£29), large, XL and XXL shirts cost $45 (£33).
The company selling merchandise at his LA gig says it was an error.
"There was a mistake in size pricing at [Wednesday] night's show," according to a representative for Live Nation. "Harry and his team were unaware and this has now been rectified."
Harry Styles opened his North America tour in San Francisco on Tuesday before playing at the Greek Theatre in Los Angeles on Wednesday.
But on social media, fans weren't happy about the difference in pricing.
The One Direction singer's next solo concert is on Nashville on Monday.
According to TMZ, Live Nation are taking legal action against the makers of unauthorised Harry Styles merchandise ahead of his gig in Tennessee.
He then plays 10 more dates in the US and Canada including performances in Chicago, Boston and New York.
He then returns to Europe at the end of October before flying to Asia, Australia and New Zealand in November.