Winter dormancy is an adaptative mechanism that temperate and boreal trees have developed to protect their meristems against low temperatures. In apple trees (Malus domestica), cold temperatures induce bud dormancy at the end of summer/beginning of the fall. Apple buds stay dormant during winter until they are exposed to a period of cold known as a chilling requirement. Once the chilling requirement is satisfied, dormancy is released, and buds can resume growth (budbreak) and initiate flowering in response to warm temperatures in spring. In the annual model plant species Arabidopsis thaliana, the thermo-regulation of flowering-time is strongly controlled by the epigenetic and post-transcriptional modification of floral-regulators genes mediated by small RNAs. Small RNAs modulate temperature responses also in woody plant species, such as grapevine, poplar, and pear. However, how small RNAs are involved in genetic networks of temperature-mediated to regulate dormancy and budbreak in fruit tree species remains unclear. To study the role of small RNAs on the control of apple dormancy, we performed a small RNA sequencing on bud samples during a time-course experiment. Using the method “TraPR” (Trans-kingdom, rapid, affordable Purification of RISCs), 373 different potential micro RNAs (miRNAs) were identified, including 105 known apple miRNAs. A total of 39 of them were differentially expressed during the dormancy cycle, suggesting their role in this process. The possible targets were identified in silico and classified according to their potential molecular function. Remarkably, targets of the identified miRNAs were related to growth control and hormonal signaling, cell wall modification, global transcriptional and post-transcriptional regulation, among other significant pathways. In conclusion, we identified several apple miRNAs and their targets potentially involved in genetic networks controlling dormancy and budbreak in fruit tree species.