In many tree species especially the rooting-recalcitrant woody perennials, the adventitious root (AR) in the juvenile phase can be easily induced by exogenous auxin, but AR formation becomes recalcitrant in the adult phase. Also, it is reported that the γ-aminobutyric acid (GABA) inhibits primary root growth in Arabidopsis and the AR formation in poplar (Populus ssp). So far, how GABA affects or is affected by the ontogenetic phase or auxin remains unclear. Here, we used an apple rootstock, Malus xiaojinensis, and tobacco (Nicotiana benthamiana) to investigate this question. We first analyzed the content of GABA, the activity of GABA synthetic enzyme GAD, and the expression of the coding gene MxGADs, respectively, in leafy cuttings of juvenile and adult phase. Next, the effect of exogenous GABA on AR formation was examined in in vitro shoots of M. xiaojinensis and tobacco. Interestingly, significant and consistent increases in GABA concentration, GAD activity, and expression of MxGAD genes in response to exogenous indole butyric acid (IBA) were detected in adult-phase cuttings, but not in juvenile-phase cuttings. Exogenous GABA application inhibited the AR formation by delaying rooting time and reducing root number and the total root length in in vitro shoots of both M. xiaojinensis and tobacco. The expression of MxPIN members increased in response to IBA application, but these changes were restrained by the addition of GABA. These results indicate that both the loss of juvenility and IBA are required to trigger GABA accumulation. GABA may affect the AR formation as a co-actor by inhibiting polar auxin transport. Together, these findings facilitate the understanding of the regulatory network among GABA, juvenility, and auxin signaling on the AR formation.