Ethylene plays an important role in apple fruit development and its biosynthesis is catalyzed by the two enzymes ACS (1-aminocyclopropane-1-carboxylate synthase) and ACO (1-aminocyclopropane-1-carboxylic acid oxidase). Within the apple ACS gene family, at least two members, MdACS1 and MdACS3, are expressed in apple fruit tissues. While MdACS1 expresses only at late ripening stages corresponding to a sudden increase of ethylene production, a typical feature of system-II ethylene biosynthesis, the expression of MdACS3 can be detected as early as 6 weeks before physiological maturity. The objective of this study was to characterize the cultivar-specific dynamics of MdACS3 expression at both preharvest and postharvest stages, its relationship with MdACS1 activation, and its roles in apple fruit ripening and quality. Based on the transcript profiles during 8-week on-tree maturation and ripening, two MdACS3 expression patterns could be clustered among 12 apple cultivars. Most of the cultivars in pattern 1 showed high level expression with a steadily increasing trend, and most of those in pattern 2 exhibited low level expression with a transient peak at or before physiological maturity. These two expression patterns appeared to correlate with fruit ripening season and fruit firmness change during ripening. Unlike MdACS1, the expression of MdACS3 was stimulated by 1-MCP treatment, indicating a negative feedback regulation mechanism.