Route 99 begins where North Washington Street becomes New Rutherford Avenue on the north side of the Charlestown Bridge. This occurs at the intersection with Chelsea Street, situated above the northbound tunnel of U.S. Route 1. Route 99 travels as a limited-access highway through Charlestown along New Rutherford Avenue, intersecting with ramps for U.S. Route 1 and passing under the Gilmore Bridge that connects Charlestown to Cambridge.
Route 99 originates at the intersection of North Washington Street and Chelsea Street on the northern approach to the Charlestown Bridge. From there, it runs as a controlled-access road through Charlestown along New Rutherford Avenue, meeting with ramps for U.S. Route 1 and passing beneath the Gilmore Bridge linking Charlestown to Cambridge.