Abstract Nuclear HER2 (N-HER2) predicts resistance to HER2-targeted therapy and poor prognosis of breast cancer patients, and the underlying mechanisms remain unclear. Here, we show that high expression of p21-activated kinase 5 (PAK5) is associated with HER2-targeted therapy resistance and poor outcomes of breast cancer patients. Excitingly, we find an increase in N-HER2 protein expression in patients with high PAK5 expression, who demonstrate resistance to trastuzumab treatment. PAK5 phosphorylates methyltransferase METTL14 on serine 399 to enhance m6A modification of lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), leading to increased MALAT1 stability. The stabilized MALAT1 inhibits ubiquitin-proteasomal degradation of the N-HER2 by affecting the interaction of deubiquitinase USP8 and N-HER2, thereby promoting N-HER2 accumulation. Moreover, HER2 upregulates the expression of PAK5 and MALAT1, activating the HER2-MALAT1 positive feedback loop. Importantly, PAK5 promotes the therapeutic resistance of HER2-positive breast cancer cells by increasing N-HER2 protein both in vitro and vivo. These findings highlight PAK5 as a therapeutic target for combating trastuzumab resistance in HER2-positive breast cancer.