diff --git a/ci/docker/conda-python-emscripten.dockerfile b/ci/docker/conda-python-emscripten.dockerfile
index 47ff550cd59..f1d0c201e90 100644
--- a/ci/docker/conda-python-emscripten.dockerfile
+++ b/ci/docker/conda-python-emscripten.dockerfile
@@ -17,21 +17,26 @@
 
 ARG repo
 ARG arch
-ARG python="3.12"
+ARG python="3.13"
 FROM ${repo}:${arch}-conda-python-${python}
 
 ARG selenium_version="4.15.2"
-ARG pyodide_version="0.26.0"
+ARG pyodide_version="0.28.1"
 ARG chrome_version="latest"
-ARG required_python_min="(3,12)"
-# fail if python version < 3.12
+ARG required_python_min="(3,13)"
+# fail if python version < 3.13
 RUN echo "check PYTHON>=${required_python_min}" && python -c "import sys;sys.exit(0 if sys.version_info>=${required_python_min} else 1)"
 
-# install selenium and recent pyodide-build and recent python
+RUN apt-get update -y -q && \
+    apt-get install -y -q --no-install-recommends \
+        libatomic1 && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
 
 # needs to be a login shell so ~/.profile is read
 SHELL ["/bin/bash", "--login", "-c", "-o", "pipefail"]
 
+# install selenium and recent pyodide-build and recent python
 RUN python -m pip install --no-cache-dir selenium==${selenium_version} && \
     python -m pip install --no-cache-dir --upgrade pyodide-build>=${pyodide_version}
 
@@ -46,9 +51,9 @@ RUN bash /arrow/ci/scripts/install_emscripten.sh ~ /pyodide
 # make sure zlib is cached in the EMSDK folder
 RUN source ~/emsdk/emsdk_env.sh && embuilder --pic build zlib
 
-# install node 20 (needed for async call support)
+# install node 22 (needed for async call support and JSPI)
 # and pthread-stubs for build, and unzip needed for chrome build to work
-RUN conda install nodejs=20  unzip pthread-stubs make -c conda-forge
+RUN conda install nodejs=22  unzip pthread-stubs make -c conda-forge
 
 # install chrome for testing browser based runner
 COPY ci/scripts/install_chromedriver.sh /arrow/ci/scripts/
diff --git a/dev/tasks/tasks.yml b/dev/tasks/tasks.yml
index e41d20e4034..93da971f09b 100644
--- a/dev/tasks/tasks.yml
+++ b/dev/tasks/tasks.yml
@@ -849,7 +849,7 @@ tasks:
     params:
       env:
         UBUNTU: 22.04
-        PYTHON: 3.12
+        PYTHON: 3.13
       image: conda-python-emscripten
 
   test-conda-python-3.11-hypothesis:
diff --git a/docker-compose.yml b/docker-compose.yml
index 3c2ea37de3e..29ea0491129 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -930,10 +930,10 @@ services:
         arch: ${ARCH}
         clang_tools: ${CLANG_TOOLS}
         llvm: ${LLVM}
-        pyodide_version: "0.26.0"
+        pyodide_version: "0.28.1"
         chrome_version: "134"
         selenium_version: "4.15.2"
-        required_python_min: "(3,12)"
+        required_python_min: "(3,13)"
         python: ${PYTHON}
     shm_size: *shm-size
     volumes: *ubuntu-volumes
diff --git a/docs/source/developers/cpp/emscripten.rst b/docs/source/developers/cpp/emscripten.rst
index d41b69aa6f0..785c9b0a67c 100644
--- a/docs/source/developers/cpp/emscripten.rst
+++ b/docs/source/developers/cpp/emscripten.rst
@@ -34,9 +34,9 @@ activate it using the commands below (see https://emscripten.org/docs/getting_st
    git clone https://github.com/emscripten-core/emsdk.git
    cd emsdk
    # replace <version> with the desired EMSDK version.
-   # e.g. for Pyodide 0.26, you need EMSDK version 3.1.58
+   # e.g. for Pyodide 0.28, you need EMSDK version 4.0.9
    # the versions can be found in the Makefile.envs file in the Pyodide repo:
-   # https://github.com/pyodide/pyodide/blob/10b484cfe427e076c929a55dc35cfff01ea8d3bc/Makefile.envs
+   # https://github.com/pyodide/pyodide/blob/0db5ff79f310694a7d72ae0b3279e9809ab836d6/Makefile.envs
    ./emsdk install <version>
    ./emsdk activate <version>
    source ./emsdk_env.sh