diff --git a/tools/ci_build/github/azure-pipelines/templates/linux-wasm-ci.yml b/tools/ci_build/github/azure-pipelines/templates/linux-wasm-ci.yml
index 8456ee42d2190..2edc357c905c1 100644
--- a/tools/ci_build/github/azure-pipelines/templates/linux-wasm-ci.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/linux-wasm-ci.yml
@@ -45,9 +45,21 @@ jobs:
     name: ${{ parameters.PoolName }}
   variables:
     buildArch: x64
+    # command line arguments for all builds
     CommonBuildArgs: '--parallel --config ${{ parameters.BuildConfig }} --skip_submodule_sync --build_wasm --use_extensions --cmake_extra_defines onnxruntime_WEBASSEMBLY_DEFAULT_EXTENSION_FLAGS=ON ${{ parameters.ExtraBuildArgs }}'
-    NonJsepBuildArgs: '--use_webnn --target onnxruntime_webassembly --skip_tests'
-    JsepBuildArgs: '--use_jsep --use_webnn --target onnxruntime_webassembly --skip_tests'
+    # command line arguments for non-JSEP builds
+    NonJsepCommonBuildArgs: '--enable_wasm_native_eh'
+    # command line arguments for JSEP builds
+    JsepCommonBuildArgs: '--use_jsep --use_webnn'
+
+    ${{ if eq(parameters.BuildConfig, 'Debug') }}:
+      # Debug build
+      NonJsepBuildArgs: '$(NonJsepCommonBuildArgs)'
+      JsepBuildArgs: '$(JsepCommonBuildArgs)'
+    ${{ else }}:
+      # Release build
+      NonJsepBuildArgs: '$(NonJsepCommonBuildArgs)'
+      JsepBuildArgs: '$(JsepCommonBuildArgs) --target onnxruntime_webassembly --skip_tests --enable_wasm_api_exception_catching'
     runCodesignValidationInjection: false
     TODAY: $[format('{0:dd}{0:MM}{0:yyyy}', pipeline.startTime)]
     ORT_CACHE_DIR: $(Agent.TempDirectory)/ort_ccache
@@ -117,7 +129,7 @@ jobs:
       ${{ else }}:
         AdditionalKey: wasm | ${{ parameters.BuildConfig }}
       CacheDir: $(ORT_CACHE_DIR)/wasm
-      Arguments: '$(CommonBuildArgs) --build_dir $(Build.BinariesDirectory)/wasm'
+      Arguments: '$(CommonBuildArgs) $(NonJsepBuildArgs) --build_dir $(Build.BinariesDirectory)/wasm'
       DisplayName: 'Build and test (node)'
       WithCache: ${{ parameters.WithCache }}
 
@@ -129,7 +141,7 @@ jobs:
       ${{ else }}:
         AdditionalKey: wasm_threads | ${{ parameters.BuildConfig }}
       CacheDir: $(ORT_CACHE_DIR)/wasm_threads
-      Arguments: '$(CommonBuildArgs) --build_dir $(Build.BinariesDirectory)/wasm_threads --enable_wasm_threads'
+      Arguments: '$(CommonBuildArgs) $(NonJsepBuildArgs) --build_dir $(Build.BinariesDirectory)/wasm_threads --enable_wasm_threads'
       DisplayName: 'Build and test (node) (threads)'
       WithCache: ${{ parameters.WithCache }}
 
@@ -141,7 +153,7 @@ jobs:
       ${{ else }}:
         AdditionalKey: wasm_simd_threads | ${{ parameters.BuildConfig }}
       CacheDir: $(ORT_CACHE_DIR)/wasm_simd_threads
-      Arguments: '$(CommonBuildArgs) --build_dir $(Build.BinariesDirectory)/wasm_simd_threads --enable_wasm_simd --enable_wasm_threads --wasm_run_tests_in_browser'
+      Arguments: '$(CommonBuildArgs) $(NonJsepBuildArgs) --build_dir $(Build.BinariesDirectory)/wasm_simd_threads --enable_wasm_simd --enable_wasm_threads --wasm_run_tests_in_browser'
       DisplayName: 'Build and test (browser) (simd + threads)'
       WithCache: ${{ parameters.WithCache }}
 
@@ -153,7 +165,7 @@ jobs:
       ${{ else }}:
         AdditionalKey: wasm_simd | ${{ parameters.BuildConfig }}
       CacheDir: $(ORT_CACHE_DIR)/wasm_simd
-      Arguments: '$(CommonBuildArgs) --build_dir $(Build.BinariesDirectory)/wasm_simd --enable_wasm_simd'
+      Arguments: '$(CommonBuildArgs) $(NonJsepBuildArgs) --build_dir $(Build.BinariesDirectory)/wasm_simd --enable_wasm_simd'
       DisplayName: 'Build and test (node) (simd)'
       WithCache: ${{ parameters.WithCache }}
 
@@ -166,7 +178,7 @@ jobs:
         ${{ else }}:
           AdditionalKey: training_wasm_simd | ${{ parameters.BuildConfig }}
         CacheDir: $(ORT_CACHE_DIR)/training_wasm_simd
-        Arguments: '$(CommonBuildArgs) --build_dir $(Build.BinariesDirectory)/training_wasm_simd --enable_training_apis --enable_wasm_simd --target onnxruntime_webassembly --skip_tests'
+        Arguments: '$(CommonBuildArgs) $(NonJsepBuildArgs) --build_dir $(Build.BinariesDirectory)/training_wasm_simd --enable_training_apis --enable_wasm_simd --target onnxruntime_webassembly --skip_tests'
         DisplayName: 'Build (training + simd)'
         WithCache: ${{ parameters.WithCache }}
 
@@ -179,7 +191,7 @@ jobs:
         ${{ else }}:
           AdditionalKey: wasm_simd_jsep | ${{ parameters.BuildConfig }}
         CacheDir: $(ORT_CACHE_DIR)/wasm_simd_jsep
-        Arguments: '$(CommonBuildArgs) --build_dir $(Build.BinariesDirectory)/wasm_simd_jsep --enable_wasm_simd $(JsepBuildArgs)'
+        Arguments: '$(CommonBuildArgs) $(JsepBuildArgs) --build_dir $(Build.BinariesDirectory)/wasm_simd_jsep --enable_wasm_simd'
         DisplayName: 'Build (simd + JSEP)'
         WithCache: ${{ parameters.WithCache }}
     - template: build-linux-wasm-step.yml
@@ -190,7 +202,7 @@ jobs:
         ${{ else }}:
           AdditionalKey: wasm_simd_threads_jsep | ${{ parameters.BuildConfig }}
         CacheDir: $(ORT_CACHE_DIR)/wasm_simd_threads_jsep
-        Arguments: '$(CommonBuildArgs) --build_dir $(Build.BinariesDirectory)/wasm_simd_threads_jsep --enable_wasm_simd --enable_wasm_threads $(JsepBuildArgs)'
+        Arguments: '$(CommonBuildArgs) $(JsepBuildArgs) --build_dir $(Build.BinariesDirectory)/wasm_simd_threads_jsep --enable_wasm_simd --enable_wasm_threads'
         DisplayName: 'Build (simd + threads + JSEP)'
         WithCache: ${{ parameters.WithCache }}