21-year-old Amuri Greene was held without bail.
He's accused of firing from the back of a moped as the child's family was standing on the street corner in East Williamsburg on April 1.
The baby, Kiaori Patterson-Moore, was struck in the head by a bullet as she sat in her stroller.
The man who prosecutors say was driving the moped, 18-year-old Mathew Rodriguez, was arraigned Tuesday on second-degree murder charges as well.
As Rodriguez was walked out of the 90th Precinct on Tuesday morning, he professed his innocence 15 times.
"I didn't do it, I didn't know it was going to happen...it's not my fault, I didn't pull the trigger," he told awaiting reporters.