Mitochondrial DNA has been adopted as a versatile genetic marker all over the globe and provides a unique maternal ancestry portrait of a person’s genetic pin code. Overall knowledge of mtDNA profiles of worldwide populations can benefit population genetics and forensic sciences. Consequently, this study was designed to establish the mtDNA profiles of the Shin ethnic group in Gilgit-Baltistan, the northern most territory of Pakistan. Phlebotomy was performed for a total of 79 maternally unrelated Shin volunteers. Genomic DNA was extracted from whole blood samples and subjected to PCR amplification using specific primers for the control region of mtDNA (covering positions 16024–16569 and 1–576), including the three hypervariable segments (HVS1, HVS2, HVS3). The PCR products were subjected to cycle sequencing and further evaluated through computational analysis. A total of 75 different haplotypes were identified in Shin people; among them, 72 were unique and 3 were shared by more than one individual. This study revealed the predominance of West Eurasian lineages in the Shin population (59.49%), followed by South Asian lineages (25.32%) and then East and Southeast Asian lineages (15.19%). Shin population presented a high genetic diversity of 0.9996 and a low random match probability of 0.0129. To the best of our knowledge, this is the first report of mtDNA profiles of the Shin population, providing a complementing dataset for curative generation of future mtDNA databases in Pakistan.