diff --git a/packages/eui/.loki/reference/chrome_desktop_Editors_Syntax_EuiCodeBlock_Virtualized_Code_Block_Scrolling.png b/packages/eui/.loki/reference/chrome_desktop_Editors_Syntax_EuiCodeBlock_Virtualized_Code_Block_Scrolling.png
new file mode 100644
index 00000000000..82bd8e647dc
Binary files /dev/null and b/packages/eui/.loki/reference/chrome_desktop_Editors_Syntax_EuiCodeBlock_Virtualized_Code_Block_Scrolling.png differ
diff --git a/packages/eui/.loki/reference/chrome_mobile_Editors_Syntax_EuiCodeBlock_Virtualized_Code_Block_Scrolling.png b/packages/eui/.loki/reference/chrome_mobile_Editors_Syntax_EuiCodeBlock_Virtualized_Code_Block_Scrolling.png
new file mode 100644
index 00000000000..cde7dc97114
Binary files /dev/null and b/packages/eui/.loki/reference/chrome_mobile_Editors_Syntax_EuiCodeBlock_Virtualized_Code_Block_Scrolling.png differ
diff --git a/packages/eui/changelogs/upcoming/9196.md b/packages/eui/changelogs/upcoming/9196.md
new file mode 100644
index 00000000000..25e65cad883
--- /dev/null
+++ b/packages/eui/changelogs/upcoming/9196.md
@@ -0,0 +1,3 @@
+**Bug fixes**
+
+- Fixed virtualized `EuiCodeBlock` rendering blank lines when content updates if scrolled.
diff --git a/packages/eui/src/components/code/code_block.stories.tsx b/packages/eui/src/components/code/code_block.stories.tsx
index 8baced4b9d4..12fdb3ec6b3 100644
--- a/packages/eui/src/components/code/code_block.stories.tsx
+++ b/packages/eui/src/components/code/code_block.stories.tsx
@@ -6,15 +6,19 @@
  * Side Public License, v 1.
  */
 
-import React from 'react';
+import React, { useEffect, useState } from 'react';
 import type { Meta, StoryObj, ReactRenderer } from '@storybook/react';
 import type { PlayFunctionContext } from '@storybook/csf';
+import { css } from '@emotion/react';
 
 import { within } from '../../../.storybook/test';
 import { LOKI_SELECTORS } from '../../../.storybook/loki';
+import { mathWithUnits } from '../../global_styling';
 
 import { EuiCodeBlock, EuiCodeBlockProps } from './code_block';
 import { expect, userEvent } from '@storybook/test';
+import { EuiButton } from '../button';
+import { EuiFlexGroup, EuiFlexItem } from '../flex';
 
 const meta: Meta<EuiCodeBlockProps> = {
   title: 'Editors & Syntax/EuiCodeBlock',
@@ -148,3 +152,97 @@ export const HighContrast: Story = {
 ],`,
   },
 };
+
+/* This Story verifies that updated data in a virtualized code block is
+rendered correctly and not cut-off after scrolling */
+export const VirtualizedCodeBlockScrolling: Story = {
+  tags: ['vrt-only'],
+  parameters: {
+    loki: {
+      chromeSelector: LOKI_SELECTORS.portal,
+    },
+    codeSnippet: {
+      skip: true,
+    },
+  },
+  // use dark mode to better visualize container boundaries
+  globals: { colorMode: 'dark' },
+  render: function Render() {
+    const [response, setResponse] = useState('{}');
+    const [isLoading, setIsLoading] = useState(false);
+
+    const handleSubmit = async () => {
+      setIsLoading(true);
+
+      try {
+        const res = await fetch('https://jsonplaceholder.typicode.com/posts');
+        const data = await res.json();
+
+        setResponse(JSON.stringify(data, null, 2));
+      } catch (error) {
+        console.error(error);
+      } finally {
+        // delay to keep VRT images more stable
+        setTimeout(() => {
+          setIsLoading(false);
+        });
+      }
+    };
+
+    useEffect(() => {
+      handleSubmit();
+    }, []);
+
+    useEffect(() => {
+      // scroll the code block after response updates to test if virtualization
+      // calculates the scroll height and position correctly
+      const pre = document.querySelector('.euiCodeBlock__pre');
+      if (pre) {
+        pre.scrollBy({
+          top: 75,
+        });
+
+        // trigger a second load after scroll to simulate potential issues
+        setTimeout(() => {
+          handleSubmit();
+        }, 10);
+      }
+    }, [response]);
+
+    return (
+      <EuiFlexGroup
+        direction="row"
+        gutterSize="m"
+        css={({ euiTheme }) => css`
+          block-size: calc(
+            100vh - ${mathWithUnits(euiTheme.size.base, (x) => x * 2)}
+          );
+        `}
+      >
+        <EuiFlexItem grow={false}>
+          <EuiButton
+            type="submit"
+            iconType="sortRight"
+            isLoading={isLoading}
+            onClick={handleSubmit}
+          >
+            Submit
+          </EuiButton>
+        </EuiFlexItem>
+        <EuiFlexItem grow={2}>
+          <EuiCodeBlock
+            language="json"
+            fontSize="s"
+            paddingSize="m"
+            isCopyable={true}
+            lineNumbers
+            isVirtualized
+            overflowHeight="100%"
+          >
+            {response}
+          </EuiCodeBlock>
+        </EuiFlexItem>
+      </EuiFlexGroup>
+    );
+  },
+};
diff --git a/packages/eui/src/components/code/code_block_virtualized.tsx b/packages/eui/src/components/code/code_block_virtualized.tsx
index bf81f69fe7d..1c2756c1261 100644
--- a/packages/eui/src/components/code/code_block_virtualized.tsx
+++ b/packages/eui/src/components/code/code_block_virtualized.tsx
@@ -32,28 +32,31 @@ export const EuiCodeBlockVirtualized = ({
   preProps: HTMLAttributes<HTMLPreElement>;
   codeProps: HTMLAttributes<HTMLElement>;
 }) => {
+  // NOTE: Don't inject other content (e.g. a label) inside this outer virtualized
+  // container as react-window requires this to be stable for scroll calculations.
+  // Instead, inject it into the inner virtualized element.
   const VirtualizedOuterElement = useMemo(
     () =>
-      forwardRef<any, any>(({ style, children, ...props }, ref) => (
-        <pre style={logicalStyles(style)} {...props} ref={ref} {...preProps}>
-          {label}
-          {children}
-        </pre>
+      forwardRef<any, any>(({ style, ...props }, ref) => (
+        <pre style={logicalStyles(style)} {...props} ref={ref} {...preProps} />
       )),
-    [preProps, label]
+    [preProps]
   );
 
   const VirtualizedInnerElement = useMemo(
     () =>
       forwardRef<any, any>(({ style, ...props }, ref) => (
-        <code
-          style={logicalStyles(style)}
-          {...props}
-          ref={ref}
-          {...codeProps}
-        />
+        <>
+          {label}
+          <code
+            style={logicalStyles(style)}
+            {...props}
+            ref={ref}
+            {...codeProps}
+          />
+        </>
       )),
-    [codeProps]
+    [codeProps, label]
   );
 
   const virtualizationProps = {