FortiManager Firmware : Upgrading from FortiManager v4.0 MR3 : Step 4: Upgrade FortiOS devices
 
Step 4: Upgrade FortiOS devices
Upgrade all FortiOS v4.0 MR3 devices to v4.0 MR3 Patch Release 12 or later. See FortiOS v4.0 MR3 Patch Release 12 Release Notes for the upgrade procedure.