Main Prison
Mountjoy Prison is constructed along a radial design with four main wings, A through D, each of which have three landings, as well as an underground basement landing. The wings are connected to a central circle, known simply as 'the circle'. When originally built in 1850 it had 500 cells each of which was designed for single capacity. Many parts of the original building have either been renovated or destroyed. At the time of the 2009 inspection, there were 371 cells in the main unit of the prison. These are the original cells which were built in 1850 for single occupancy. Their size varies from 3.91m x 2.06m to 3.43m x 2.06m. The prison was built with in-cell sanitation but this was removed in 1939 when it was deemed that 'prisoners were using too much water'. However, all cells in the main jail have in-cell sanitation following refurbishment in the period 2010 to 2015. These cells contain a toilet, a sink, a television and a small kettle.

Facilities in the prison include gymnasiums, computer classes, carpentry, masonry and a wide variety of school activities such as music, drama and cookery. Prisoners can undertake to complete academic exams in the school such as Junior Certificate, Leaving Certificate and even Open University. Additionally, there is an on-site kitchen and bakery where trusted inmates are given employment under supervision.

Medical Unit
The Medical Unit, otherwise referred to as the drug detoxification unit, is a three storied structure. It provides accommodation for sixty prisoners in forty-eight single person cells and three cells that can accommodate up to four people. All the cells in this unit have in-cell sanitation facilities. It is equipped with medical facilities, classrooms and kitchen facilities. The Inspector of Prisons reported in 2009 that this unit was bright and clean and did not suffer from overcrowding.

Controlled Behavioural Unit
The Controlled Behavioural Unit, known as the CBU or the Block, is used for unruly prisoners or those on punishment and is located in the 'D' Base, underneath the D wing. This includes 24-hour lock-up, with the exception of one hour of open air exercise, and no integration with other inmates.

Separation Unit
The Separation Unit had 35 cells. It also had kitchen facilities a shower block and a laundry. In the late 1980s, inmates diagnosed with HIV or AIDS were housed in the separation unit. This policy was brought to an end on 1 January 1995. Following the unit's refurbishment in 1997, all cells had in-cell sanitation. The separation unit was closed indefinitely in 2014 following an inspection by the Inspector of Prisons.

Mountjoy Campus
The Mountjoy Campus is home to three other separate penal facilities.

Dóchas Centre
St. Patrick's Institution
Training Unit
People associated with Mountjoy
A former governor was Charles Arthur Munro, brother of the Edwardian satirist Saki.

The schizophrenic French surrealist playwright Antonin Artaud was briefly detained in Mountjoy before his deportation from Ireland as "a destitute and undesirable alien".

Thomas Ashe was also a former inmate of the jail for his involvement in the Easter rising 1916. After a protest of starvation he was transferred across the street to the Mater Misericordiae Hospital on 25 September 1916 where he died a few hours after arrival.

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