A girl of the same age, believed to be his twin sister, was also found critically injured at a flat in Finsbury Park.
Police were called to Wilberforce Road in Finsbury Park on Saturday night and discovered the toddlers who were subsequently rushed to a hospital in East London. A baby girl now remains in a critical condition and is receiving specialist medical care.
Police says the children have yet to be formally identified.
A post-mortem examination on the boy is due to take place soon and police said his family had been informed of his death.
They added that inquiries were under way to "establish the full circumstances of the incident" and said that no arrests had been made.
Detective Chief Inspector Dave Whellams, of the Homicide and Major Crime Command, said: "Whilst we remain in the early stages of the investigation, a man has now been arrested".
A police helicopter was searching for a suspect this morning, NPAS London tweeted.
Neighbours recalled hearing a woman screaming for herlp shortly before police arrived, she is believed to be their mother Cristinela Datcu. I heard someone was shouting.
The neighbour said she later saw two young children being carried out of the building, with one being held very close to a member of the emergency services.
"She kept on shouting". I do not know what she was shouting. "It's really tense", she said.
Anyone with information can call 020 8345 3775 or Crimestoppers on 0800 555 111.