The academic lyceum was established based on the Resolution No. 204 of the Cabinet of Ministers of the Republic of Uzbekistan dated May 13, 1998, "On Measures for Organizing Secondary Specialized and Vocational Education in the Republic of Uzbekistan," as well as Resolution No. 473 dated October 29, 2003, "On Additional Measures to Ensure the Consistent Transition to General Secondary and Secondary Specialized Vocational Education." Additionally, it was founded following Order No. 111 of the Center for Secondary Specialized and Vocational Education dated July 5, 2006, and Resolution No. 133 of the Navoiy Regional Administration dated June 1, 2006. Initially, it was named the "No. 2 Academic Lyceum under the Navoi State Mining Institute."

From 2006 to 2009, the educational institution was led by Odil Egamberdiyevich Khojamurodov. During these years, a solid foundation was laid for the establishment of the educational institution, its socio-economic development, academic and spiritual growth, financial and economic stability, and the formation of a cohesive and professional team.

According to the Resolution No. PQ-3290 of the President of the Republic of Uzbekistan dated September 26, 2017, "On Further Improving the System of Targeted Preparation of Candidates for Higher Educational Institutions," the No. 2 Academic Lyceum under the Navoi State Mining Institute was transferred under the jurisdiction of the Navoi State Mining Institute and was renamed the Academic Lyceum of the Navoi State Mining Institute.

From 2009 to 2017, the academic lyceum was headed by Ra’no Zokirovna Hayitova. Under her leadership, continuous efforts were made to achieve comprehensive success. Special attention was given to maintaining discipline in education and moral upbringing, enhancing the quality of education, expanding the team of highly qualified teachers, and fostering the mentor-apprentice tradition to cultivate professional educators.

Following the Presidential Resolution No. PQ-186 dated March 31, 2022, "On the Establishment of the Navoi State University of Mining and Technology," the academic lyceum was renamed the Academic Lyceum of the Navoi State University of Mining and Technology.

Since 2017, the academic lyceum has been led by Feruza Rahmonqulovna Tadjitdinova. During this period, the lyceum’s prestige has reached a high level nationwide. The integration of new innovative pedagogical technologies into the teaching process, the effectiveness of specialized subject clubs, and the strong academic performance of lyceum students have significantly contributed to this success. From 2017 to 2019, the percentage of graduates who gained admission to higher education institutions was 90%, while from 2020 to 2024, this figure increased to 95-100%. Under the fair leadership of Feruza Rahmonqulovna and the dedicated efforts of a cohesive and highly skilled teaching staff, the academic lyceum has also expanded internationally, establishing collaborations with several foreign higher education institutions.

From its establishment until 2024, more than 8,500 graduates of the academic lyceum have successfully completed higher education and are actively contributing to various prestigious organizations and institutions in Uzbekistan’s economy and society.