The alleged incident took place around 2:30 p.m. in the Bronx at the 149th Street-Grand Concourse station in the borough's Melrose neighborhood.
The woman -- Jessica Mixon of the Bronx, according to WABC -- was taken to Bronx-Lebanon Hospital Center in the Bronx for a psychological evaluation.
She faces charges of reckless assault on a child, reckless endangerment and abandonment.
The toddler was taken to Lincoln Medical Center in the Bronx in serious but stable condition. He suffered a cut to his left eye and an abrasion to his head.
WABC reported that witnesses called police and alerted two officers that were inside the subway station at the time.
The NYPD said the officers noticed the mother at the top of the subway staircase.