The 'Everything Is Everything' singer has been charged with skipping returns in 2005, 2006 and 2007.
According to court documents obtained by TMZ, Hill earned over $1.8 million (£1.2m) during that period, and now stands to owe up to $300,000 (£193,000) in fines.
She is also in danger of a jail sentence of one year for each count of tax evasion.
Hill is due to appear in court for the offence on June 29.
The singer experienced legal troubles in August 2011, when guitarist Jay Gore sued her with claims that she abused staff during a European tour.
The reclusive singer recently performed a rare one-off gig in April at London's IndigO2.
Watch Lauryn Hill in the video for 'Doo-Wop (That Thing)' below: