The Tun Hussein Onn National Eye Hospital was established in 1986 by the late Yang Amat Berhormat (YAB) Tun Hussein Onn, the third Prime Minister of Malaysia and the Chairman of Malaysia Association for Blindness (MAB) (1975 - 1990).

Tun Hussein Onn realised the necessity of having a dedicated eye hospital to provide professional eye care to Malaysians, to educate them on prevention measures to avoid unnecessary blindness, and to manage disorders which may lead to loss of vision. In 1988, the hospital's services were further enhanced through the establishment of sub-speciality clinics, as well as a focus on training and research.

In 1996, THONEH set up the National Eye Bank to fulfil Malaysia's dire need of corneal transplants, and to help in the procurement of eye donors. The Eye Bank became affiliated with the International Federation of Eye and Tissue Banks (IFETB), which assists individuals, groups, and governments in developing national eye and tissue banking programs that service their citizenries and help increase the quality of life for their people and the people of the world.

THONEH established an in-house college, the National Institute of Ophthalmic Sciences (NIOS) in 1997 to ensure that the Malaysian public receives proper eye care from well-equipped and trained staff and doctors. This educational arm of THONEH consists of the School of Ophthalmic Medical Personnel, the School of Optometry, and the School of Post Graduate Studies and Research. Since its inception, NIOS has produced numerous graduates who are the cream of the crop in their field of study.

Today, THONEH's facilities are located in a six-storey tower block and a five-storey podium block. There are three floors of outpatient clinics, supported by a 40-bedded inpatient ward department, four operating theatres, and a day recovery area. NIOS, the diagnostic centres, the eye bank, laser centre, cornea and refractive surgery centre, and an auditorium occupy the rest of the infrastructure. These facilities enhance THONEH's ability to offer better and up-to-date treatment and solutions in a comfortable and soothing ambiance. In 2008, THONEH obtained its ISO 9001:2008 certified accreditations from United Kingdom Accreditation Service (UKAS), Comitefrancaisd'accreditation (COFRAC) and Standards Malaysia, giving assurance to its patients that the services offered are in line with international standards.

Recognised for consistently providing excellent services in eye care, THONEH was awarded the prestigious Brand Laureate, SMEs Chapter Award 2009, and the Best Brands Healthcare Eye Hospital by the Asia Pacific Brand Foundation (APBF). In 2010, THONEH was recognised with the Malaysia Health Tourism Award presented by YB Dato Seri Liow Tiong Lai on behalf of the Ministry of Health.

In February 2014, THONEH arrived at another level of recognition by attaining the Joint Commission International (JCI) accreditation, an international mark and endorsement for quality patient care and patient safety.

THONEH is also one of the founding members of the ASEAN Association of Eye Hospitals (AAEH), alongside the American Eye Center, Jakarta Eye Centre, Rutnin Eye Hospital, and Singapore National Eye Centre. The AAEH aims to promote co-operation between eye hospitals and eye centres to make ASEAN a Centre of Excellence for Ophthalmology, comparable to the best eye hospitals in the world.