Mitochondria, which have critical roles in energy metabolism and oxidative regulation, also have a role in immune regulation including T cell activation, NET formation, inflammation, and apoptosis. More than 50% of those with systemic lupus erythematosus (SLE) have lupus nephritis due to kidney damage from immune complex deposition. Disease severity is reported to be greater in certain lineages. Mitochondrial DNA (mtDNA) haplogroups, which reflect maternal lineages, may modulate immune balance and disease outcomes in SLE. Methods: DNA was extracted from 25 consecutive, consenting pediatric patients that fulfilled the 1997 criteria for SLE and their maternal mitochondrial DNA (mtDNA) haplogroups were determined through next-generation sequencing (NGS). Results: This study evaluated the associations between mtDNA haplogroups, lupus nephritis, and organ damage in four mtDNA haplogroups: African (n = 5), Amerindian (n = 12), Asian (n = 4), and Caucasian (n = 4). Clinical data, SLE Disease Activity Index (SLEDAI-2K), SLICC Damage Index (SDI), and renal biopsy findings were analyzed. Median SLEDAI-2K scores were higher in Amerindian (10) and African (8) patients than in the Caucasian (5.5) and Asian (3) groups, with significant differences between Amerindian vs. Caucasian (p = 0.045) and Amerindian vs. Asian (p = 0.008). Irreversible organ damage (SDI > 1) was more frequent in Amerindian (54%) and African (40%) patients. Lupus nephritis occurred most often and most severely (Class III–IV, CKD) in the Amerindian (85%) and African (80%) groups, while Caucasian and Asian patients more often showed milder, membranous disease without CKD. Conclusion: Although limited by the small sample size, pediatric SLE severity and renal involvement were found to be greater in Amerindian and African mtDNA haplogroups, suggesting that mitochondrial lineage may contribute to ethnic disparities in SLE.