The 18-year-old man died while being treated for third degree burns, said government health system spokesman Rosendo Gaytan yesterday.
Another 33 workers remain hospitalised, six of them in critical condition, he said.
The blast Thursday on the second floor of the Dulces Blueberry factory caused the floor to collapse, injuring people working downstairs.
The factory, which employs 300 people, produces gummy bears, jelly beans, peach rings and other sweets that are sent to El Paso, Texas, across the border from Ciudad Juarez.
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Firefighters and rescue crews didn't find any more victims inside the building after searching it late into the night Thursday, city officials said. Workers' relatives, however, say one employee is unaccounted for.
Worker Jose Gonzalez said the explosion was so strong it threw him against a wall.
"When I felt the explosion, I flew and landed against a wall," Gonzalez said. "There was a hole on the wall and I ran out through it. I went back in because I heard people crying and screaming."
Manuel Lopez arrived at the factory as the explosion happened. He had gone there to visit his father who worked there.
"Everything came flying out, even the walls," Lopez said.
"The fire was really strong but I still went in and helped."
Ciudad Juarez is a manufacturing hub and the assembly plants there employ many of its residents.