Self-compatibility (SC) in a naturally self-incompatible fruit tree species is a highly interesting trait for breeding objectives and a valuable tool for investigating the mechanism of the gametophytic self-incompatibility (GSI) system. This study focused on apple (Malus × domestica Borkh.), carried out γ-ray mutagenesis, and succeeded in producing a self-compatible mutant. The reciprocal pollination test showed that a pollen factor is involved in its SC. Results on S-RNase genotyping by allele-specific PCR amplification of the progenies of the mutant revealed that SC in the mutant was not caused by a nonfunctional pollen S factor in either one of the S-haplotypes but presumably by an S-chromosomal alteration (i.e., reciprocal translocation of an S-haplotype or a partial S-chromosomal duplication). Amplicon sequencing of S-haplotypes of progeny individuals suggested that the most probable S-chromosomal alteration in the mutant could be a translocation of an S-haplotype to a nonhomologous chromosome; such S-chromosomal alteration made it possible for the mutant to produce S-heteroallelic pollen grains that overcome self-incompatibility by competitive interaction between the two different S-factors in a pollen grain. These results supported the idea of a “collaborative non-self-recognition system by multiple factors” based on the GSI system in apple, similar to those in Pyrus of Rosaceae and Solanaceae. Implications for breeding self-compatible apple using the mutant induced in this study are briefly discussed.