diff --git a/plugins/mcp-server/src/com/intellij/mcpserver/McpToolsMarkdownExporter.kt b/plugins/mcp-server/src/com/intellij/mcpserver/McpToolsMarkdownExporter.kt
index e0889d124b47..ec8efe3d680a 100644
--- a/plugins/mcp-server/src/com/intellij/mcpserver/McpToolsMarkdownExporter.kt
+++ b/plugins/mcp-server/src/com/intellij/mcpserver/McpToolsMarkdownExporter.kt
@@ -22,20 +22,22 @@ object McpToolsMarkdownExporter {
         appendLine("## ${category.shortName}")
         appendLine()
         for (tool in categoryTools) {
-          appendToolSection(tool, headingLevel = 3)
+          appendToolSection(tool, headingLevel = 3, omitFirstDescriptionLine = false)
         }
       }
     }
   }
 
   /**
-   * Generates a single-page markdown document for one MCP tool: top-level heading, full description,
+   * Generates a single-page markdown document for one MCP tool: top-level heading, description,
    * input parameters table, and output schema table (when present).
    *
-   * Use together with [generateMarkdownTree] when emitting per-tool reference files.
+   * [omitFirstDescriptionLine] drops the first non-blank line of the description while keeping the rest.
+   * The per-tool files of [generateMarkdownTree] pass `true`: that first line is already shown as the
+   * tool's summary in the index, so repeating it in the per-tool file is duplication and wasted context.
    */
-  fun generateMarkdownForTool(tool: McpTool): String = buildString {
-    appendToolSection(tool, headingLevel = 1)
+  fun generateMarkdownForTool(tool: McpTool, omitFirstDescriptionLine: Boolean = false): String = buildString {
+    appendToolSection(tool, headingLevel = 1, omitFirstDescriptionLine = omitFirstDescriptionLine)
   }
 
   /**
@@ -71,7 +73,7 @@ object McpToolsMarkdownExporter {
     }
     for ((_, categoryTools) in byCategory) {
       for (tool in categoryTools) {
-        result["$TREE_TOOLS_SUBDIR/${tool.descriptor.name}.md"] = generateMarkdownForTool(tool)
+        result["$TREE_TOOLS_SUBDIR/${tool.descriptor.name}.md"] = generateMarkdownForTool(tool, omitFirstDescriptionLine = true)
       }
     }
     return result
@@ -99,10 +101,15 @@ object McpToolsMarkdownExporter {
     "Nested `*` is scoped to the parent object's presence — required nested fields are only guaranteed " +
     "when the optional parent object is emitted."
 
-  private fun StringBuilder.appendToolSection(tool: McpTool, headingLevel: Int) {
+  private fun StringBuilder.appendToolSection(tool: McpTool, headingLevel: Int, omitFirstDescriptionLine: Boolean) {
     val heading = "#".repeat(headingLevel)
     appendLine("$heading ${tool.descriptor.name}")
-    appendLine(tool.descriptor.description.trimIndent().escapeLineBreaks().escapeMarkdown())
+    val description =
+      if (omitFirstDescriptionLine) tool.descriptor.description.dropFirstNonBlankLine()
+      else tool.descriptor.description.trimIndent()
+    if (description.isNotBlank()) {
+      appendLine(description.escapeLineBreaks().escapeMarkdown())
+    }
     appendLine()
     appendLine("$heading# Parameters")
     val inputRows = tool.descriptor.inputSchema.toSchemaTableRows()
@@ -243,7 +250,20 @@ object McpToolsMarkdownExporter {
     return required.mapNotNull { (it as? JsonPrimitive)?.content }.toSet()
   }
 
-  private fun String.escapeLineBreaks(): String = 
+  /**
+   * Drops the first non-blank line (and any blank lines preceding it) and returns the remaining body,
+   * trimmed. That first line is the tool summary shown in the index ([generateMarkdownTree]); see
+   * [generateMarkdownForTool]'s `omitFirstDescriptionLine`. Returns an empty string for a single-line
+   * description.
+   */
+  private fun String.dropFirstNonBlankLine(): String {
+    val lines = trim().lines()
+    val firstNonBlank = lines.indexOfFirst { it.isNotBlank() }
+    if (firstNonBlank < 0) return ""
+    return lines.drop(firstNonBlank + 1).joinToString("\n").trim()
+  }
+
+  private fun String.escapeLineBreaks(): String =
     replace("\r\n", "<br/>").replace("\n", "<br/>").replace("\r", "<br/>")
 
   private fun String.escapeMarkdown(): String = replace("|", "\\|")
diff --git a/plugins/mcp-server/src/com/intellij/mcpserver/toolsets/general/ExecutionToolset.kt b/plugins/mcp-server/src/com/intellij/mcpserver/toolsets/general/ExecutionToolset.kt
index 6e5e341b135d..3bd40734e801 100644
--- a/plugins/mcp-server/src/com/intellij/mcpserver/toolsets/general/ExecutionToolset.kt
+++ b/plugins/mcp-server/src/com/intellij/mcpserver/toolsets/general/ExecutionToolset.kt
@@ -97,8 +97,8 @@ class ExecutionToolset : McpToolset {
 
   @McpTool(name = ExecutionToolNames.EXECUTE_RUN_CONFIGURATION)
   @McpDescription("""
-    |Run either an existing run configuration by name or a temporary run configuration created from a code location
-    |(`filePath` + `line`) in the current project, then wait up to specified timeout for it to finish.
+    |Run either an existing run configuration by name or a temporary run configuration created from a code location (`filePath` + `line`) in the current project, then wait up to specified timeout for it to finish.
+    |
     |Use this tool with either a configuration name returned by `get_run_configurations`, or with a run point
     |(`filePath` + `line`) returned by `get_run_configurations(filePath = ...)`.
     |
diff --git a/plugins/mcp-server/tests/testSrc/com/intellij/mcpserver/McpToolsMarkdownExporterTest.kt b/plugins/mcp-server/tests/testSrc/com/intellij/mcpserver/McpToolsMarkdownExporterTest.kt
index caef8ddbba6f..c532bee168c7 100644
--- a/plugins/mcp-server/tests/testSrc/com/intellij/mcpserver/McpToolsMarkdownExporterTest.kt
+++ b/plugins/mcp-server/tests/testSrc/com/intellij/mcpserver/McpToolsMarkdownExporterTest.kt
@@ -296,16 +296,37 @@ class McpToolsMarkdownExporterTest {
   }
 
   @Test
-  fun generateMarkdownTreePerToolFileMatchesGenerateMarkdownForToolOutput() {
+  fun generateMarkdownTreePerToolFileMatchesFirstLineOmittedSingleToolOutput() {
     val t = setMarkerTool()
 
     val result = McpToolsMarkdownExporter.generateMarkdownTree(listOf(t))
     assertEquals(
-      McpToolsMarkdownExporter.generateMarkdownForTool(t),
+      McpToolsMarkdownExporter.generateMarkdownForTool(t, omitFirstDescriptionLine = true),
       result.getValue("$TREE_TOOLS_SUBDIR/set_marker.md"),
     )
   }
 
+  @Test
+  fun generateMarkdownTreePerToolFileDropsFirstDescriptionLineButKeepsBody() {
+    val t = startTaskTool(
+      description = "Starts a task using the supplied configuration.\nReturns the task handle.",
+    )
+
+    val result = McpToolsMarkdownExporter.generateMarkdownTree(listOf(t))
+    val index = result.getValue(TREE_INDEX_FILE)
+    val perTool = result.getValue("$TREE_TOOLS_SUBDIR/start_task.md")
+
+    assert(index.contains("Starts a task using the supplied configuration.")) {
+      "Index should keep the first description line: $index"
+    }
+    assert(!perTool.contains("Starts a task using the supplied configuration.")) {
+      "Per-tool file should drop the first description line (it lives in the index): $perTool"
+    }
+    assert(perTool.contains("Returns the task handle.")) {
+      "Per-tool file should keep the rest of the description body: $perTool"
+    }
+  }
+
   @Test
   fun generateMarkdownTreeEmptyListReturnsOnlyIndexHeaderAndLegend() {
     val result = McpToolsMarkdownExporter.generateMarkdownTree(emptyList())