Stem rust of wheat, caused by fungus Puccinia graminis f. sp. tritici (Pgt), is an economically important disease of wheat. Detection of Pgt race Ug99 (TTKSK) in Uganda in 1998, its spread and further evolution has increased the global stem rust research in the last decade. Thirteen races belonging to Ug99 lineages, that have added virulence to additional resistance genes, are spread to 13 countries as far as South Africa to Yeman and Egypt. There is a consistent need to identify, characterize and strategically utilize new sources of resistance genes, especially those conferring durable adult-plant resistance (APR) in developing resistant cultivars. The aim of our study was to determine the basis of resistance to stem rust in a semi-dwarf wheat breeding line ‘Kenya Fahari/2*Kachu’ that derived part of its APR from the tall variety ‘Kenya Fahari’ and showed high levels of APR to Ug99 and other races currently prevalent in Kenya. A recombinant inbred line (RIL) population of 198 lines from the cross ‘Apav’ × ‘Kenya Fahari/2*Kachu’ was developed and phenotyped for stem rust resistance during the 2016 and 2018 off and main seasons in Njoro, Kenya. RIL population and parents were genotyped using DArT-GBS markers, and QTL analysis was conducted. Previously known stem rust resistance locus Sr58 (=Lr46/Yr29), derived from ‘Kachu’ mapped on chromosome 1BL, explained 12.2 to 20.0% of variation for stem rust severity. A stem rust resistance locus on chromosome 6AS was also identified, which explained 13.5 to 35.9% of stem rust variation. This QTL is putatively a new stem rust resistance locus derived from Kenya Fahari. The frequency of advanced wheat lines carrying the 6AS locus in combination with other APR genes is increasing in CIMMYT breeding materials through phenotypic selection at Njoro under high disease pressure. Markers flanking 6AS locus will be converted into reliable and diagnostic kompetitive allele specific PCR (KASP) markers for marker assisted selection in breeding programs. A third stem rust resistance QTL on chromosome 2AS was also identified, however has smaller effects (5.9-8.2%) compared to Sr58 and 6AS QTL. Our results also show that high levels of APR to stem rust requires combining multiple APR genes that individually have small to intermediate effects. Because ‘Kenya Fahari’ and other related varieties remained moderately resistant to stem rust in Kenya, it is likely that high levels of resistance in new wheat materials possessing 6AS QTL as a component could lead to resistance durability.