[5] Scientists at the Government Regional Public Analyst Laboratory on the college campus were the first to discover that Maggi noodles contain too much monosodium glutamate (MSG), resulting in a high-profile case in the media.

[7] It is a major centre for treating encephalitis,[8] a disease that has seen regular outbreaks during the monsoon season in the Gorakhpur region.

Other medical practitioners have blamed the hospital's negligence as a major factor behind the high number of child deaths.

The deaths attracted media attention and generated political controversy in August 2017, when 296 children died, including 77 of encephalitis.

Mahanti, accused the college principal, R.K. Singh, of impeding the normal functioning of the institute by frequently going on leave.

In August 2011, Mahanti's successor K. Ravindra Nayak made serious allegations against Singh, including improper award of maintenance contracts, purchase of hospital supplies at inflated rates, misappropriation of funds from various government schemes, irregularities in job appointments, and non-payments or delayed payments to other parties despite the availability of sanctioned funds.

Kushwaha, who held the charge of the pediatrics department and the encephalitis ward, complained about the malfunctioning ventilators installed by the contractor GT Enterprises during 2008–2009.

[14] A report found dogs roaming around the hospital chambers and beds being shared by multiple patients in the pediatric ward.

The college spent part of the funds to hire 135 researchers, doctors, and paramedics focused on encephalitis treatment.

[4] In August 2017, it was reported that an average of 300 child patients were being admitted to the 50-bed pediatric Intensive Care Unit (ICU) every month.

It emerged that the dues were not paid despite several letters by the supplier to various officials of the state administration, including the Chief Minister Adityanath.

[11] In 2009, scientists from the United States Centers for Disease Control and Prevention visited the area to take samples to identify the virus.

[11] According to Govindakarnavar Arunkumar of the Manipal Institute of Virus Research, in Gorakhpur, the scrub typhus was not diagnosed and treated during the early stages, ultimately triggering difficult-to-cure brain inflammation.