Water shortage is one of the main limiting factors in apple (Malus domestica Borkh.) production. Although dopamine is produced in plants and has been linked with response to abiotic stress, the underlying mechanism remains unknown. In this study, physiological analyses revealed that pretreatment with 100 μM dopamine alleviated drought stress in apple seedlings. Dopamine inhibited the degradation of photosynthetic pigments and increased net photosynthetic rate under drought stress. Dopamine also reduced H2O2 content, possibly through direct scavenging and by mediating the antioxidant enzyme activity. Seedlings pretreated with dopamine had higher sucrose and malic acid contents but lower starch accumulation in their leaves. RNA-Seq analysis identified 1052 differentially expressed genes (DEGs) between non-treated and dopamine-pretreated plants under drought. An in-depth analysis of these DEGs revealed that dopamine regulated the expression of genes related to metabolism of nitrogen, secondary compounds, and amino acids under drought stress. In addition, dopamine may improve apple drought tolerance by activating Ca2+ signaling pathways through increased expression of CNGC and CAM/CML family genes. Moreover, analysis of transcription factor expression suggested that dopamine affected drought tolerance mainly through the regulation of WRKY, ERF, and NAC transcription factors.