Data from the city's Department of Health and Mental Hygiene shows that as of Oct. 24 -- the latest date for which data is available -- visits for children under age 5 reached 88.9 per 100,000 visits.
This is the highest number seen since Dec. 26, 2021, when the city was in the middle of the omicron wave, according to the data.
It comes as doctors worry the nation could face a "tripledemic" this fall and winter as cases of flu and respiratory syncytial virus, RSV, continue to rise and, although COVID-19 infections have not yet begun to spike, they have in years prior begun to around Thanksgiving.
"What we're seeing in New York is actually reflected in what we're seeing across the country right now, which is unprecedented levels of respiratory illness in our pediatric populations," said Dr. John Brownstein, an epidemiologist and chief innovation officer at Boston Children's Hospital and an ABC News contributor.
He said that because of restrictions due to the COVID-19 pandemic -- such as masking, social distancing and school closures -- which have since mostly been lifted, children are now being exposed to viruses that were circulating at low levels for two years.
"While we spent the better half of more than two years trying to protect our kids from COVID, likely those efforts meant lack of exposure to other respiratory illnesses and, with mixing of kids, we're seeing a respiratory season that is very much unlike what we've seen historically," Brownstein said.
Between the week ending Sept. 17, 2022 and the week ending Oct. 15, 2022, RSV positive test results have risen from about 400 to more than 1,600.
This follows national trends seen in the United States, with cases rising from 3,389 to 7,917 over the same period, according to data from the Centers for Disease Control and Prevention.
Brownstein said RSV surges during most winters, but this year it's occurring earlier than usual.
The same thing is being seen with the flu. Although overall flu activity is low in the city, it's starting to rise, according to the report.
Over the same four-week period, positive flu tests have spiked from more than 150 to around 400.
Because of multiple circulating viruses, and the threat of new COVID variants emerging, Brownstein said it's possible the rate of ER visits for young kids in New York City -- and other areas of the country -- could exceed what was seen during the peak of the omicron wave.
To prevent hospitalizations, Brownstein urged parents to make sure their children are up to date on their vaccines, stay home if sick, practice good hand hygiene and only visit the ER if they are experiencing severe symptoms to help ease the burden on hospitals.
"We want to make sure parents are utilizing emergency departments appropriately," he said. "Not all kids necessarily need to go to the emergency department for these viruses. We are going to be concerned about hospital capacity just to handle this influx. So, if possible, make sure to call your pediatrician to understand what treatment options are [available]."