The Deerfield-based drugstore chain said the systems were restored at all of Walgreen's 8,200 pharmacies by 1 p.m., said Jim Graham a spokesman.
The outage, which affected all Walgreens pharmacies across the country, occurred during a routine database update that went awry, requiring the entire system to shut down, Graham said.
Walgreen worked throughout the morning and early afternoon to restore the database. The company filled more than 800 million prescriptions in its most-recent fiscal year.
Shares were down 2 cents at $61.05 in afternoon trading.