Lentil, Lens culinaris Medic., is an important cool season grain legume because of the high level of iron (Fe) in its seeds since Fe deficiency is widespread and causes anemia. Thus, identifying genes controlling Fe concentration in the seed was needed for mapping in the lentil genome. The objectives of this study were to (i) detect phenotypic variation in Fe concentration in the seeds of a recombinant inbred line (RIL) population, (ii) construct a high-density linkage map using genotyping by sequencing (GBS), and (iii) identify localization of the quantitative trait loci (QTLs) controlling genes for Fe concentration in lentil seeds. In this work, Fe concentration in seeds of the RIL population ranged from 37.2 to 175.7 mg per kg. A linkage map was constructed covering 497.1 cM with a total of 4177 SNP markers. A total of 21 QTL regions explaining 5.9%-14.0% of the phenotypic variation were identified on six linkage groups (LG1, 2, 4, 5, 6, and 7) with LOD scores ranging from 3.00 to 4.45. This is the first report on the construction of a high-density linkage map through GBS and mapping of QTLs controlling iron uptake in lentil. Identification of these genomic regions will be useful for future biofortification studies to develop new varieties of lentil with high Fe concentrations.