Fruit trees have a long juvenile period after germination before flowering and fruit set. In spite of its horticultural importance, the physiological and molecular mechanisms of juvenility in fruit tree development are unknown; therefore, the relationship between the expression of the AGAMOUS-LIKE6 (AGL6) homolog and juvenility was investigated in apple (Malus domestica Borkh.). The results of sequence alignment, the phylogenetic tree, and Southern blot analysis suggested that MdMADS11 is an AGL6 ortholog in apple. An increase in the abundance of the mRNA of MdMADS11, which promotes flowering, corresponded to changes in leaf area and serration with the transition from the juvenile to adult phase in apple seedlings. In contrast, the abundance of mRNA of MdJOINTLESS, which may suppress flowering, decreased with the phase transition. Expression analysis of adult apple trees suggested that MdMADS11 also plays a role in seasonal flower initiation and floral organ formation in the adult phase. The results provide new insight into the molecular mechanism of the phase transition between juvenile and adult fruit trees.