diff --git a/scripts/install.ps1 b/scripts/install.ps1
index 7645af00da..4706778cc9 100644
--- a/scripts/install.ps1
+++ b/scripts/install.ps1
@@ -1060,9 +1060,10 @@ function Install-Repository {
         # directory OR a symlink OR a submodule-style gitfile -- and also when
         # it's a broken stub left over from a failed previous install (e.g.
         # a partial Remove-Item that couldn't delete a locked index.lock).
-        # Validate the repo properly by asking git itself.  Two checks
-        # belt-and-braces: rev-parse AND git status.  If either fails the
-        # repo is broken and we fall through to a fresh clone.
+        # Validate the repo properly by asking git itself.  Three checks
+        # belt-and-braces: rev-parse (work tree), git status, and a resolvable
+        # HEAD (an initial commit).  If any fails the repo is broken and we
+        # fall through to a fresh clone.
         $repoValid = $false
         if (Test-Path "$InstallDir\.git") {
             Push-Location $InstallDir
@@ -1077,7 +1078,17 @@ function Install-Repository {
                 $null = & git -c windows.appendAtomically=false status --short 2>&1
                 $statusOk = ($LASTEXITCODE -eq 0)
 
-                if ($revParseOk -and $statusOk) {
+                # An interrupted previous clone leaves a repo with NO initial
+                # commit. rev-parse/status still succeed there, but the update
+                # path's `git stash` (and later `git checkout`) abort with
+                # "You do not have the initial commit yet" and fail the install
+                # (#40998). Require a resolvable HEAD so such partial checkouts
+                # are treated as broken and re-cloned fresh below.
+                $global:LASTEXITCODE = 0
+                $null = & git -c windows.appendAtomically=false rev-parse --verify HEAD 2>&1
+                $hasCommit = ($LASTEXITCODE -eq 0)
+
+                if ($revParseOk -and $statusOk -and $hasCommit) {
                     $repoValid = $true
                 }
             } catch {}
diff --git a/scripts/install.sh b/scripts/install.sh
index e24e6537b6..0527025499 100755
--- a/scripts/install.sh
+++ b/scripts/install.sh
@@ -1092,6 +1092,15 @@ show_manual_install_hint() {
 clone_repo() {
     log_info "Installing to $INSTALL_DIR..."
 
+    # An interrupted previous clone leaves a .git with no initial commit, where
+    # the update path's `git stash` / `git checkout` abort with "You do not
+    # have the initial commit yet" and fail the install (#40998). Drop such a
+    # partial checkout so the fresh-clone path below handles it cleanly.
+    if [ -d "$INSTALL_DIR/.git" ] && ! git -C "$INSTALL_DIR" rev-parse --verify HEAD >/dev/null 2>&1; then
+        log_warn "Existing checkout at $INSTALL_DIR has no commits (interrupted clone) -- replacing it."
+        rm -rf "$INSTALL_DIR"
+    fi
+
     if [ -d "$INSTALL_DIR" ]; then
         if [ -d "$INSTALL_DIR/.git" ]; then
             log_info "Existing installation found, updating..."