Background: Targeted therapy with tyrosine kinase inhibitors (TKIs) benefits most patients with stromal tumors; however, the effects of TKIs in patients with rare cases of gastrointestinal stromal tumors (GISTs) with platelet-derived growth factor receptor alpha (PDGFRA) exon 12 mutations are unclear. Our report of a case treated with multiline TKIs (included ripretinib) may provide some experience into the future management of rare GIST with PDGFRA 12 exon mutation.Case Description: We report the case of a patient (42-year-old female) with a PDGFRA exon 12-mutated GIST who underwent multiple surgeries and multiple lines of TKI therapy. This patient had intra-abdominal recurrence after imatinib, which was used as the 1st-line targeted drug treatment for 7 months after radical surgery, and had widespread metastases in the abdominal cavity after sunitinib, which was used as the 2nd-line targeted drug treatment for 6 months after the second radical surgery. For this advanced GIST patient with extensive intraperitoneal metastasis and rare PDGFRA 12 exon mutation, we then selected ripretinib as the 3rd-line targeted drug therapy to treat the patient. Up to the last follow-up in September 2021, the patient continued to take drugs without obvious complaints of discomfort or adverse events.Conclusions: This case showed that patients with PDGFRA exon 12-mutated GISTs are less likely to benefit from current conventional TKIs, and ripretinib treatment should be considered preferred to regorafenib or even sunitinib according to each patient's situation. However, the limitation of our case is that the patient's second recurrent lesion was not genetically tested to determine the presence of secondary mutation. Further, if a patient's tumor has a high risk of adverse biological behaviors, such as high mitotic figures, vascular tumor thrombus, succinate dehydrogenase B (SDHB) was negative, and regional lymph node metastasis, consideration should be given to shortening the postoperative follow-up interval to 2 months or even 1 month.