The Stratus ftServer Series family supports Windows Server 2008 & 2003. Reliability improvements in newer Windows releases have brought a level of reliability to the operating system that is consistent with the system reliability of the fault-tolerant ftServer systems. Stratus enhances the standard Windows operating system environment with unique failsafe software features, but does not modify the base Windows operating system or compromise compatibility in any way. All ftServer models have passed the testing required to receive the "Designed for Microsoft Windows" logo and are listed on Microsoft's Windows Hardware Compatibility List (HCL). This testing ensures that ftServer systems are fully compatible with the Windows operating system and virtually any Windows-compatible application. All Stratus-enhanced device drivers are also tested and receive digital signatures to guarantee full Windows compatibility.

Stratus will pre-install Windows Server 2003 at the factory if the software is purchased from Stratus. Optionally, customers may purchase their own copy of Windows and use the ftServer System Software CD to install the Windows operating system along with Stratus failsafe software enhancements. Stratus tests and integrates Microsoft Windows Service Packs as they are released and also provides testing and guidance for use of Microsoft Hotfixes.