The body of the six-year-old boy was recovered a short time after the pair were swept away, but a seach continues for the other, aged 10, officials said.
The Los Angeles Times reported search-and-rescue efforts were continuing along the stretch of the Vernal Fall footbridge, a popular stop beneath the waterfall along the park's most-used Mist Trail, said park spokesman Scott Gediman.
There were 15 members of an extended family, from Southern California, visiting the area when tragedy struck.
The 10-year-old's death marks the third drowning at the park this year, Gediman said.
Last year, three people died after being swept over Vernal Fall itself.
"Horrible. Horrible. Horrible situation," Gediman was quoted in the Los Angeles Times.
"These situations are always difficult, but because they're boys...".
ABC News reported the family began their hike at the Happy Isles Trailhead and stopped near the footbridge about 3 p.m. on Wednesday to cool off in the river, Gediman said.
At some point, the boys were caught in the current and swept downstream.
While signs at the trailhead warn that the river can be dangerous, people often are drawn to the water's edge, and are unaware that the current is surprisingly strong.