ARID1A (AT-rich interaction domain 1A), a key subunit of the switch/sucrose non-fermentable (SWI/SNF) chromatin remodeling complex, is frequently mutated in cancers. However, effective clinical treatments for patients with this mutation are limited, highlighting a need for therapeutic strategies. Here, we identify Werner syndrome adenosine 5'-triphosphate-dependent helicase (WRN) as a critical vulnerability in ARID1A-mutated cancers. Upon genetic and pharmacological inhibition of WRN, ARID1A-mutated cells had defective checkpoint kinase 1 (Chk1)-mediated DNA damage signaling, resulting in compensatory checkpoint kinase 2 (Chk2) activation, leading to G₁ phase arrest and apoptosis, whereas ARID1A-proficient cells underwent Chk1-dependent G₂-M arrest. Additional p21 inhibition in the context of WRN suppression promoted cell cycle reentry of G₁-arrested ARID1A-mutated cells, resulting in enhanced cytotoxicity through mitotic catastrophe. The antitumor efficacy of WRN inhibition alone and in combination with p21 inhibition was validated using cell line-based xenograft and patient-derived xenograft mouse models. Our findings define WRN as a selective therapeutic target in ARID1A-mutated cancers and suggest a combinatorial strategy of WRN and p21 inhibition as a therapeutic approach.