Some 33 people were hurt, with a number taken to hospital for evaluation, although emergency services said the injuries were only light.
The kids suffered injuries like whiplash, bruising and torso pain after slamming into the guard rail as they sat in rollercoaster cars.
Police and park staff are investigating the cause of the accident.
One eyewitness said that the waiting train was stuck, while the other train quickly approached from behind and hit it hard.
The rollercoaster, the Tren de la Mina or "Mine Train", reaches a height of 17.5m and travels 450m through waterfalls at a maximum speed of 55km per hour, according to the theme park's website.
Spanish theme park accident: Trains collide on Madrid rollercoaster
One eye-witness said the those on the ride couldn't anticipate the crash because they were wearing virtual reality headsets.
The injured are being taken to three different hospitals throughout Madrid.
The Wild West-themed ride is both a normal roller coaster and a virtual reality experience.
The shocking accident happened at 2.30pm on a runaway mine-cart-themed ride at Parque de Attraciones in Madrid, Spain.
Opened in 1969, the Parque de Atracciones of Madrid extends over 20 hectares in the Casa del Campo, the main park of the capital.
Canada's Trudeau meets tiny namesake, the son of refugees
The boy's parents, Afraa Hajj Hammoud and Mohammed Bilal , arrived in Canada in February of 2016 and named their newborn in May. Muhammad and Afraa Bilal arrived in Canada in February past year with their two young children after escaping war-torn Syria.
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