The shooting happened around noon at a home in the 900 block of East Hamilton Street.
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Police say officers arrived at the scene to find the 3-year-old boy suffering from a gunshot wound.
They rushed him to the hospital but the child ultimately died from his injuries.
Allentown police say the investigation is active and ongoing.
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They say there is "no physical threat" to the community.
Anyone with information is asked to contact detectives at 610-437-7721 or the Police Desk at 610-437-7753 (ext 1).
Anonymous text tips can also be sent via the Tip411 App available on the Allentown Police Facebook page or via the Allentown Police Department website.