Inspectors found the company's average over-billing was $2.15, according to the Department of Agriculture, Trade and Consumer Protection.
A store in Greenfield had the highest overcharge $20 for a device to reduce telemarketing calls.
Trade and consumer protection administrator Janet Jenkins said the department has found pricing problems with the drug store going back to the 1990s. She said the deal for civil forfeitures and fees was reached in the last few weeks.
Walgreens did not admit to any wrongdoing in the deal.
Company spokeswoman Carol Hively said in a statement the mistakes were largely caused by human error, such as not taking signs down after a sale ended.
Story continues below advertisement