The child, Tristian Hutchins, died last week. He was shot outside a Third Ward shopping center more than a month ago.
The suspect, 18-year-old Devonte Lockett, spent the night in jail.
Lockett was arrested Thursday night and is now charged with murder in the death of Hutchins.
Hutchins was shot in the head in a March 1 drive-by shooting as his mother ran inside a Third Ward salon.
The boy's 5-year-old sister was shot in the leg. She survived. A third sibling was not injured in the shooting.
At a press conference Friday, Houston Police Chief Art Acevedo, Mayor Sylvester Turner and Congresswoman Sheila Jackson Lee discussed Lockett's arrest.
"We've had a lot of tips coming in," Acevedo said.
He added that the department is looking for possibly other suspects in the fatal drive-by shooting.
Turner also pledged an additional $1 million for HPD.
"I have authorized an additional $1 million in police overtime to work in communities to solve this and other crimes and build relationships with diverse neighborhoods," Turner said.
TIMELINE: Children killed by gun violence in Houston
Lockett is no stranger to police.
According to documents, he was previously charged for evading arrest, possession of a controlled substance, and for carrying a handgun in a motor vehicle.
Hutchins was the 10th child shot and killed in Houston in the past year, police say.
News of the child's murder sent shockwaves through the community, with even Houston Mayor Sylvester Turner and Houston Police Chief Art Acevedo weighing in on the crime.
Mayor Turner tweeted after hearing the news of Lockett's arrest, saying, "Violence against our kids will not be tolerated. We will work overtime and spend whatever it takes to protect our children."
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