diff --git a/pkg/agent/agent_mcp.go b/pkg/agent/agent_mcp.go
index d04a0fdf3..3d569b2bd 100644
--- a/pkg/agent/agent_mcp.go
+++ b/pkg/agent/agent_mcp.go
@@ -317,8 +317,16 @@ func filterMCPConfigServers(
 
 	filtered := mcpCfg
 	filtered.Servers = make(map[string]config.MCPServerConfig)
+	normalizedAllowed := make(map[string]struct{}, len(allowed))
+	for serverName := range allowed {
+		name := normalizeMCPServerName(serverName)
+		if name == "" {
+			continue
+		}
+		normalizedAllowed[name] = struct{}{}
+	}
 	for serverName, serverCfg := range mcpCfg.Servers {
-		if _, ok := allowed[serverName]; ok {
+		if _, ok := normalizedAllowed[normalizeMCPServerName(serverName)]; ok {
 			filtered.Servers[serverName] = serverCfg
 		}
 	}
diff --git a/pkg/agent/agent_mcp_test.go b/pkg/agent/agent_mcp_test.go
index 5c3f67445..7c8a4cd28 100644
--- a/pkg/agent/agent_mcp_test.go
+++ b/pkg/agent/agent_mcp_test.go
@@ -172,6 +172,38 @@ func TestToolRegistryIncludesReportsOnlyRegisteredTools(t *testing.T) {
 	}
 }
 
+func TestFilterMCPConfigServersCaseInsensitivePreservesOriginalKeys(t *testing.T) {
+	mcpCfg := config.MCPConfig{
+		Servers: map[string]config.MCPServerConfig{
+			"GitHub":     {Enabled: true},
+			"filesystem": {Enabled: true},
+			"Slack":      {Enabled: true},
+		},
+	}
+	allowed := map[string]struct{}{
+		"github":     {},
+		"FILESYSTEM": {},
+	}
+
+	filtered := filterMCPConfigServers(mcpCfg, allowed)
+
+	if len(filtered.Servers) != 2 {
+		t.Fatalf("filtered.Servers = %v, want 2 entries", filtered.Servers)
+	}
+	if _, ok := filtered.Servers["GitHub"]; !ok {
+		t.Fatal("expected original GitHub config key to be preserved")
+	}
+	if _, ok := filtered.Servers["filesystem"]; !ok {
+		t.Fatal("expected filesystem config key to be preserved")
+	}
+	if _, ok := filtered.Servers["github"]; ok {
+		t.Fatal("did not expect normalized github key to replace original config key")
+	}
+	if _, ok := filtered.Servers["Slack"]; ok {
+		t.Fatal("did not expect unallowed Slack server")
+	}
+}
+
 func TestEnsureMCPInitialized_LoadFailureSetsInitErr(t *testing.T) {
 	al, cfg, _, _, cleanup := newTestAgentLoop(t)
 	defer cleanup()
diff --git a/pkg/agent/tool_allowlist.go b/pkg/agent/tool_allowlist.go
index 87ae2ee4c..7a020c82c 100644
--- a/pkg/agent/tool_allowlist.go
+++ b/pkg/agent/tool_allowlist.go
@@ -11,6 +11,24 @@ import (
 
 const dynamicMCPToolPrefix = "mcp_"
 
+func normalizeMCPServerName(name string) string {
+	return strings.ToLower(strings.TrimSpace(name))
+}
+
+func normalizedMCPServerNameSet(
+	servers map[string]config.MCPServerConfig,
+) map[string]struct{} {
+	normalized := make(map[string]struct{}, len(servers))
+	for serverName := range servers {
+		name := normalizeMCPServerName(serverName)
+		if name == "" {
+			continue
+		}
+		normalized[name] = struct{}{}
+	}
+	return normalized
+}
+
 func warnOnUnknownAgentToolDeclarations(
 	agentID, workspace string,
 	definition AgentContextDefinition,
@@ -93,13 +111,14 @@ func unknownAgentMCPServerNames(cfg *config.Config, definition AgentContextDefin
 		return nil
 	}
 
+	knownServers := normalizedMCPServerNameSet(cfg.Tools.MCP.Servers)
 	unknown := make(map[string]struct{})
 	for _, raw := range definition.Agent.Frontmatter.MCPServers {
-		name := strings.ToLower(strings.TrimSpace(raw))
+		name := normalizeMCPServerName(raw)
 		if name == "" {
 			continue
 		}
-		if _, ok := cfg.Tools.MCP.Servers[name]; ok {
+		if _, ok := knownServers[name]; ok {
 			continue
 		}
 		unknown[name] = struct{}{}
diff --git a/pkg/agent/tool_allowlist_test.go b/pkg/agent/tool_allowlist_test.go
index 46bbac2bc..4851dcaa8 100644
--- a/pkg/agent/tool_allowlist_test.go
+++ b/pkg/agent/tool_allowlist_test.go
@@ -93,3 +93,30 @@ mcpServers: [github, githb]
 		t.Fatalf("unknownAgentMCPServerNames() = %v, want [githb]", unknown)
 	}
 }
+
+func TestUnknownAgentMCPServerNamesMatchesConfigCaseInsensitively(t *testing.T) {
+	workspace := setupWorkspace(t, map[string]string{
+		"AGENT.md": `---
+mcpServers: [github, FileSystem, slak]
+---
+# Agent
+`,
+	})
+	defer cleanupWorkspace(t, workspace)
+
+	cfg := &config.Config{
+		Tools: config.ToolsConfig{
+			MCP: config.MCPConfig{
+				Servers: map[string]config.MCPServerConfig{
+					"GitHub":     {Enabled: true},
+					"filesystem": {Enabled: true},
+				},
+			},
+		},
+	}
+
+	unknown := unknownAgentMCPServerNames(cfg, loadAgentDefinition(workspace))
+	if len(unknown) != 1 || unknown[0] != "slak" {
+		t.Fatalf("unknownAgentMCPServerNames() = %v, want [slak]", unknown)
+	}
+}