Aluminum (Al) toxicity is one of the major environmental constraints to crop production in acidic soils. The objective of this study was to map quantitative trait loci (QTLs) of yield-related traits associated with tolerance to Al in wheat (Triticum aestivum L.). A recombinant inbred line population of wheat was evaluated under conditions of 800 µm aluminum chloride hexahydrate (AlCL₃.6H₂O) at tillering, stem-elongation and flowering stages. Single-locus analysis showed that 22 of 79 QTLs identified were putative. These QTLs explained 4.38–12.24% of the total variation of traits in two growing seasons. Based on two-locus analysis, 71 additive and 11 epistatic QTLs were identified, of which 34 additive and three epistatic QTLs had significant interaction with environmental effects. The greatest number of stable QTLs was related to the A genome. Stable QTLs associated with days to heading and grain yield, with no additive × environment interactions, were co-located with Al concentration (on the 2D linkage group) and 1000-grain weight (on the 6B linkage group). The markers linked to major and stable QTLs identified in the present study can be further assessed in other genetic backgrounds and environmental conditions in order to improve marker-assisted selection and Al tolerance in wheat.