Supplier Pegatron confirmed that the 15-year-old was among four workers "who died of illness in the second half of the year" in the Shanghai plant, which has about 100,000 employees
According to New York-based China Labor Watch, Shi Zhaokun died of pneumonia on October 9 at a Shanghai hospital.
He made Apple products at the factory, which demanded employees work for 12 hours each day, the group claimed.
An Apple spokeswoman in China told AFP the California-based firm sent independent officials from China and the US to conduct an investigation at the factory which found "no evidence" of a link between the deaths and working conditions.
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Pegatron officials in Taipei stressed that the company forbids the employment of child workers and that Shi used a 20-year-old relative's ID to get hired.
It has strict measures in place to verify workers' ages but the identification for Shi "had been wrongly issued", the officials said.
The company said that the deaths have been ruled non-work related by investigations conducted by its client and Shanghai's health authorities.
Pegatron produces consumer electronics such as game consoles, television sets and computers for Sony, Toshiba and other brand name vendors, as well as assembling products for Apple.