Background: Anti-PD-1 antibody combined with chemotherapy showed promising efficacy in gastric adenocarcinoma. However, little is known about biomarkers that identify clinical response. Here, we focus on genomic alteration patterns to predict response of neoadjuvant immunotherapy in patients with locally advanced gastric or gastroesophageal junction adenocarcinoma (GC/GEJC). Methods: Patients with locally advanced GC/GEJC were received 4 cycles of FOLFOX plus anti-PD-1 antibody (camrelizumab) as neoadjuvant therapy in the study. We prospectively conducted whole exome sequencing (WES) in paired biopsy specimens from enrolled patients at baseline. According to Tumor Regression Grading (TRG) assessment by postoperative pathology, patients were classified into group A (TRG0 & TRG1) and group B (TRG2 & TRG3). Results: We eventually performed WES in 23 patients who had adequate available tumor tissues. The clinical characterizations were not significantly different between two groups. All 23 cases were microsatellite stable (MSS). Alterations of AHNAK2 (50.0%/6.67%), TG (50.0%/6.67%), CTNNB1 (37.5%/0.0%) and ZFHX2 (37.5%/0.0%) significantly enriched in group A (n = 8) compared to group B (n = 15).Furthermore, we inspecting 10 hallmark oncogenic pathways, alterations of WNT pathway also occurred more frequently in group A than those of group B. Genomic alterations in WNT pathway were identified in 5 of 23 cases (21.74%), of which the most frequently mutated genes were CTNNB1 (13.04%), LRP5 (8.69%) and RNF43 (8.69%). Tumor mutation burden (TMB, p = 0.357), whole genome duplication (WGD) status (p = 0.667), copy number variant burden (p = 0.825), fraction of loss of heterozygosity (LOH) in chromosome level (p: 0.07-1), tumor neoantigen burden (TNB) (p = 0.65), HLA type (p: 0.49-1) and HLA LOH status (p: 0.37-1) were not significantly associated with neoadjuvant therapy response. Conclusions: Aberrant activation of WNT pathway was reported to be associated with immune evasion. Our study demonstrated that CTNNB1/WNT-pathway-mut may be a promising predictor for clinical response of neoadjuvant immutherapy in GC/GEJC. Clinical trial information: NCT03939962