Ben Stirland, from Consett, was pronounced dead in hospital two days after it is believed he inadvertently swallowed the plastic top.
Paramedics struggled to revive him at his Consett home. He was taken to Durham's University Hospital then moved to Newcastle General, but later died.
Staff at his school, Moorside Community Technology College, paid tribute to the popular teenager.
The youngster's mother Nathalie warned of the hidden dangers of pen tops.
'Senseless death'
Mrs Stirland, 38, a youth worker, wrote on the Friends Reunited website: "My precious, beautiful 13-year-old son died after 48 hours of trying to save him.
"My son tipped off his chair and ingested his pen lid.
"Contrary to popular belief, the safety hole is no use. Body secretions soon block this and because of the lid's shape, they easily lodge in the throat and cannot be removed quickly.
"I have lost one of the biggest parts of my life and if I can warn just one parent and stop another senseless death like this, it will have been worth posting."
The schoolboy lived with his mother, stepfather David Hodgson, 36, sister Briony and his younger brother, also called Ben.
Moorside Community Technology College head Jonathan Morris said: "Ben was a much-loved member of our community and I am proud to have been his head teacher."
The Royal Society for the Prevention of Accidents said it was a very rare incident.
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