The blast happened on Monday evening in a rural area of central Puebla state during preparations for a local festival next week, according to Diodoro Carrasco, a state government senior official in Puebla state.
The fireworks were due to be used for the local patron saint's festival on May 15 and were stored inside a house behind a church.
Nine people were killed on the spot and three more died after being taken to nearby hospitals.
The death toll stands at 14 and 22 people were injured, officials say.More news: HYS: Should Chelsea bid for Antonio Rudiger?
More than 70 other people, including many children, were injured and burned in the blast at the San Pablito market in December.
At least 14 people were killed and 22 were injured after an explosion ripped through a fireworks warehouse in Puebla, Mexico.
The tragedy in San Isidro comes four months after fire and explosions tore through a sprawling fireworks market on the outskirts of the Mexican capital, killing 33 people and wounding many more.
The area is located around 200 km south-east of Mexico City.More news: Freeze Warning, Frost Advisories in WNY
The blast was set off by a rocket fired from outside the building that struck the stored pyrotechnic material, the government said.
State governor Antonio Gali Fayad said he had ordered the authorities "to see to the wounded and give the village of San Isidro all the help necessary".
The use of fireworks during holiday festivities is very common in Mexico, sometimes with fatal consequences.
Christmas and New Year parties in many Latin American countries often wrap up with a fireworks free-for-all.More news: Lewis Hamilton mystified by lack of pace at Russian Grand Prix
The fireworks industry reports almost Dollars 10 million a month in revenue in Mexico.