Class III peroxidases (PODs) perform crucial functions in various developmental processes and in response to biotic and abiotic stresses. However, the specific roles of class III POD genes in wheat seed dormancy (SD) and germination remain elusive. Here, we identified a wheat class III POD gene, named TaPer12-3A, based on transcriptome data and expression analysis. TaPer12-3A showed decreasing and increasing expression trends with SD acquisition and release, respectively, indicating a significant association with SD and germination. It was highly expressed in wheat seeds and localized in the endoplasmic reticulum and cytoplasm. Germination tests indicated that TaPer12-3A negatively regulated SD and positively mediated germination in transgenic Arabidopsis and rice lines as well as in a wheat mutant mutagenized with ethyl methane sulfonate (EMS) in Jing 411 background. Further studies demonstrated that TaPer12-3A regulated SD and germination by interacting with gibberellin and abscisic acid biosynthesis, catabolism, and signaling pathways in transgenic rice seeds. These findings not only provide new insights for future functional analysis of TaPer12-3A in regulating wheat SD and germination but also contribute to understanding the complex regulatory mechanism involved in these processes.