To ascertain the variability in Fe and Zn concentrations in lentil (Lens culinaris Medikus ssp. culinaris) seeds, a set of 58 lentil genotypes were evaluated in randomized complete blocks at eight locations in Nepal during 2006 to 2012. Micronutrient contents of the seeds were analyzed. The mean Fe varied from 72.4 μg g−1 at Surkhet in 2009 to 98.2 μg g−1 at Rampur in 2012, and the mean Zn from 23.9 μg g−1 at Surkhet in 2012 to 85.1 μg g−1 at Parwanipur in 2009. The genotype effect and genotype × location interaction were significant for Fe (P = 0.01–0.03). For Zn, the genotype effect was significant (P = 0.008), and the genotype × location interaction was not (P = 0.46). The variance component estimates for the genotype × year interaction within locations were zero for both the minerals, indicating genotypic stability over the years. The best line for Fe was ILL7723 (81.0 μg g−1) and RL6 for Zn (56.2 μg g−1). The lines that were within the top 20% for high concentrations of both minerals were Barimasoor4, RL6, RL9, ILL8006, RL11, RL12, ILL9926, and ILL6819. The lowest concentrations of the minerals were found in Shital for Fe (74.2 μg g−1) and Black musuro for Zn (51.4 μg g−1). These results provide a useful foundation for the development of new lentil cultivars that have high mineral content and could be used to develop more nutritious varieties of lentil and reduce mineral element deficiencies in Nepal.