[3] As a consequence of the 1999 crisis that led ultimately to East Timorese independence from Indonesia, the hospital was taken over by the International Committee of the Red Cross (ICRC), which managed it until 2003, a period that included a year-long preparation for hand over.

During that period, the IRC and the government of East Timor cooperated in upgrading the hospital, including by expanding the number of wards and units, recruiting more staff, and improving medical and non-medical equipment.

The project, co-financed by the government and the European Union, and scheduled for completion in October 2007, included thorough rehabilitation of the hospital complex and construction of a new operating theatre.

The report's recommendations included a drastic change in leadership of the hospital, an improvement in management capacities, alterations to staffing practices, work organisation, supervision and control, and increased systematisation.

The program was held at a number of venues, including four of East Timor's regional reference hospitals, and then, in mid-October 2016, was carried out at HNGV.

The aim of the grant aid was to improve HNGV's healthcare service, especially for patients needing emergency or obstetrics and gynaecology care.

[11] Meanwhile, on 16 April 2019, the Deputy Minister of Primary Health Care, Élia dos Reis Amaral, swore in 17 new HNGV Heads of Department.

[13]: 14–15  On the other hand, there was a large pandemic-related decrease in visits to the outpatient department and the emergency room, caused mainly by a "lack of trust" in the health system and "increased fear" of the hospital during the pandemic.

Red Cross of East Timor) (CVTL) and HNGV of more than 115,000 items of personal protective equipment (PPE) and sanitation materials.

[14] In early 2022, the Royal Australasian College of Surgeons engaged a consultant to develop a strategic plan to improve the clinical education function at HNGV, and support the positioning of the facility as a national teaching hospital over the longer term.

On a daily basis, English (HNGV's working language), Spanish, Portuguese, Indonesian and Tetun are used in conversation and in the hospital's clinical notes.

Chronic shortages in patient transport, caused by inadequate coverage and malfunctioning ambulance and ‘multi-function vehicle’ services, are the principal barrier.

[31] Patients from remote parts of the country, including pregnant women, accident victims and those suffering from the effects of a stroke, are commonly also faced with rugged mountainous terrain, with very poor standards of infrastructure.

[34]Meta Mali went on to observe that the government through the Ministry of Health is therefore forced to spend a lot of money to pay for aeroplanes, hospital fees and accommodation costs for the safety of its people.

[34] The RACS, in collaboration with the Ministry of Health, manages a project for the provision of clinical services and training of medical staff at HNGV.

[28][35] As of 2016[update], the project involved the provision of specialists in five areas – surgery, paediatrics, emergency medicine, anaesthesia, and obstetrics and gynaecology – to assist in particular with postgraduate training of Timorese doctors and midwives.

First delivered as a pilot course in 2016, the HMP uses project-based learning to teach participants how to lead teams, and to undertake quality improvement processes across hospital units.

[42][43] HNGV is also involved in the Maternal Child Health (MCH) program run by Alola Foundation, an NGO founded in 2001 by Kirsty Sword Gusmão, a now former First Lady of East Timor.