Lithuanian Prison Service was established on 11 February 1919.

During the period of Soviet occupation, the penal enforcement system of Lithuania was an integral part of the Soviet Union’s overall penal enforcement system under the jurisdiction of the Ministry of Interior. Prison Department was renamed: first, Board of Corrective Labour Institutions, later, Board of Correctional Affairs.

After the restoration of independence in 1990 the Board of Correctional Affairs was reorganized into the Department of Correctional Affairs.

On 1 September 2000 in the course of the reform of the legal system, the penal enforcement system was transferred from the jurisdiction of the Ministry of Interior to the Ministry of Justice. The Department of Correctional Affairs regained the name it had during the interwar period of independent Lithuania - the Prison Department under the Ministry of Justice of the Republic of Lithuania.

From 1990 to 2001 Mr Jonas Blaževicius was the head of the institution. By the Order of the Minister of Justice of 17 June 2002, Mr Skirmantas Agurkis was appointed the Acting Director General of the Prison Department. From 22 April 2003 to 18 February 2005 the Prison Department was led by Mr Rimvidas Kūgis. From 28 April 2005 till 12 July 2011 Mr Saulius Vitkūnas served as the Director General of the Prison Department. From 12 July 2011 to 23 January 2012 Mr Kęstutis Širvaitis was the Acting Director General of the Prison Department. Mr Artūras Norkevičius was appointed the Director General of the Prison Department from 24 January 2012 to 8 December 2014. Since 12 January 2015 Prison Department was temporary lead by Ms Živilė Mikėnaitė who was appointed the Director General of the Prison Department on 1 June 2015 to 27 March 2017. Mr Robertas Krikštaponis headed the Prison Department from 22 December 2017 to 7 February 2019.

On 1 January 2023, as a result of the organizational reform, which started in 2022, the structure and name of the Prison Department was changed, and now the official name is Lithuanian Prison Service.

Mr Virginijus Kulikauskas is the Director General of Lithuanian Prison Service.