Conventional topical medications for recurrent aphthous ulcers (RAU) are limited due to the washing effects of saliva and activities of masticatory muscles decreasing the local effective drug concentration. To overcome this drawback, a dissolvable and layered hyaluronate (HA) microneedle (MN) patch loading recombinant bovine basic fibroblast growth factor (rbFGF) and cetylpyridinium chloride (CPC) was prepared and used for the treatment of RAU. The MN patch was prepared via a two-step casting method and subsequently characterized using fluorescence microscopy, scanning electron microscopy (SEM), and stereomicroscopy. Moreover, its mechanical properties, penetrating ability, dissolution behavior, antibacterial performance, cytotoxicity as well as ulcer healing efficacy on the rat model were determined. The results revealed that the prepared MNs possessed uniformly arranged conical needles with the drug centrally distributed in the tips. The rbFGF/CPC-loaded HA MN patch presented favorable mechanical, dissolving, and antibacterial properties and biocompatibility, increasing the growth and proliferation of fibroblasts. More importantly, this MN patch showed a higher healing effect in promoting the healing of chemical-induced RAU within five days than the control group and the conventional treatment group. The novel MN patch will have potential application prospects in the treatment of oral ulcer.