diff --git a/buildscripts/resmokeconfig/matrix_suites/generated_suites/sharding_stepdown_fcv_upgrade_downgrade_jscore_passthrough.yml b/buildscripts/resmokeconfig/matrix_suites/generated_suites/sharding_stepdown_fcv_upgrade_downgrade_jscore_passthrough.yml
index e1fc26377d9..68907bdd821 100644
--- a/buildscripts/resmokeconfig/matrix_suites/generated_suites/sharding_stepdown_fcv_upgrade_downgrade_jscore_passthrough.yml
+++ b/buildscripts/resmokeconfig/matrix_suites/generated_suites/sharding_stepdown_fcv_upgrade_downgrade_jscore_passthrough.yml
@@ -86,6 +86,10 @@ executor:
             skipEnforceFastCountOnValidate: true
     - class: CheckOrphansDeleted
     - class: FCVUpgradeDowngradeInBackground
+      shell_options:
+        global_vars:
+          TestData:
+            runningWithConfigStepdowns: true
     - class: CleanEveryN
       n: 20
 matrix_suite: true
diff --git a/buildscripts/resmokeconfig/matrix_suites/overrides/fcv_upgrade_downgrade_primary_step_down_overrides.yml b/buildscripts/resmokeconfig/matrix_suites/overrides/fcv_upgrade_downgrade_primary_step_down_overrides.yml
index 37c92749b83..0d1bb714876 100644
--- a/buildscripts/resmokeconfig/matrix_suites/overrides/fcv_upgrade_downgrade_primary_step_down_overrides.yml
+++ b/buildscripts/resmokeconfig/matrix_suites/overrides/fcv_upgrade_downgrade_primary_step_down_overrides.yml
@@ -63,6 +63,10 @@
                 skipEnforceFastCountOnValidate: true
         - class: CheckOrphansDeleted
         - class: FCVUpgradeDowngradeInBackground
+          shell_options:
+            global_vars:
+              TestData:
+                runningWithConfigStepdowns: true
         - class: CleanEveryN
           n: 20
 
diff --git a/jstests/hooks/run_fcv_upgrade_downgrade_background.js b/jstests/hooks/run_fcv_upgrade_downgrade_background.js
index ca3f0ca02b9..cd0b996dd28 100644
--- a/jstests/hooks/run_fcv_upgrade_downgrade_background.js
+++ b/jstests/hooks/run_fcv_upgrade_downgrade_background.js
@@ -34,6 +34,12 @@ const sendFCVUpDown = function (ver) {
             jsTest.log.info("setFCV: Temporarily unavailable", {e});
             return;
         }
+        if (e.code === ErrorCodes.HostUnreachable && TestData.runningWithConfigStepdowns) {
+            // The mongos may exhaust its retries due to having consecutive config stepdowns.
+            // In this case, the mongos will return a HostUnreachable error.
+            jsTest.log.info("setFCV: Host unreachable", {e});
+            return;
+        }
         if (e.code === ErrorCodes.CannotUpgrade) {
             jsTest.log.info("setFCV: Can not upgrade", {e});
             return;