In 1990 the first higher educational institution in Samtskhe-Javakheti Region – Akhaltsikhe Branch of Ivane Javakhishvili Tbilisi State University was founded. In 1991 ,,Independent University of Akhaltsikhe” was established on the basis of the existed branch which joined Akhaltsikhe Branch of Tbilisi State University as a paid educational department in 1995.
In 2002 Akhaltsikhe Branch of Ivane Javakhishvili Tbilisi State University was named as Meskheti Branch of Ivane Javakhishvili Tbilisi State University.
In 2007 Independent Higher Educational Institution – Legal Entity of Public Law Akhaltsikhe Institute was established on the basis of Meskheti branch of Tbilisi State University according to the government resolution #161.
LEPL Akhaltsikhe University has passed institutional accreditation and received the license of Higher Educational Institution in 2007.
LEPL Akhaltsikhe Institute received the Status of Teaching University in 2009 and was named as LEPL Akhaltsikhe State Teaching University according to the government resolution #183.
On December 14th, 2011 after the reorganization implemented in LEPL Akhaltsikhe State Teaching University its successor – Non-profit (Non-commercial) Legal Entity Akhaltsikhe State Teaching University was established according to the government resolution #476.
On 3rd October, 2012 after the reorganization implemented on the basis of two educational institutions – Non-profit (Non-commercial) Legal Entity Akhaltsikhe State Teaching University and Akhalqalaqi Higher Educational Institution – College Non-profit (Non-commercial) Samtskhe-Javakheti State Teaching University was established according to the government resolution #416.
On 30th July, 2013 according to the government resolution #194 Non-profit (Non-commercial) Samtskhe-Javakheti State Teaching University was reorganized to LEPL Samtskhe-Javakheti State Teaching University.
On 24th February, 2014 according to decision #8 of Higher Education Institution Accreditation Council LEPL Samtskhe-Javakheti State Teaching University was granted the status of a Higher Educational Institution – University.