On Server 2016, can i set up a cluster and install MDT so that MDT is highly available?

I am tasked with setting up a MDT server for deploying OS to 25000 endpoints. Is it possible for me set up clustering and then install MDT so MDT is HA. I am also planning to host the deployment share on a clustered HA file share.

There is an option to build distributed MDT environment, which can cover your needs. https://docs.microsoft.com/en-us/windows/deployment/deploy-windows-mdt/build-a-distributed-environment-for-windows-10-deployment

Of course, as mentioned, you can build an HA File Share and put MDT shares there. The following link might help you: https://www.starwindsoftware.com/resource-library/starwind-virtual-san-for-hyper-v-2-node-hyperconverged-scenario-with-windows-server-2016/

Architecture Overview

MDT is architected as a file share, optionally a SQL DB to track metrics, and optionally WDS for the ability to network boot your Windows PE image.

MDT is booted from whatever medium, such as USB or WDS or CD. The booted Windows PE image then reaches out to the network file share (unless it is an offline MDT instance) specified in the bootstrap.ini file. The rest happens over that file share connection.

MDT is edited from the workbench software but that software does not need to be present on any server for it to work as a server for MDT. Ideally you will only have the workbench software installed on your PAW/admin workstation, as to not increase the surface area for attack on the server.
As an example, I have spun up a raspberry pi using Ubuntu with SAMBA as the FS and placed the MDT file share on it. I also used iPXE WIMboot to allow a linux based WDS instance but that is a story for another time.

Knowing the above architecture will allow us to make the service HA and bend it to your will. So, depending on your component choices, all you may need to cluster is your file share tomake MDT HA.

High Availability for MDT Components (Links)

• File Share Clustering:
  https://docs.microsoft.com/en-us/windows-server/failover-clustering/deploy-two-node-clustered-file-server

• SQL Database (Optional, not all MDT instances use this):
  https://docs.microsoft.com/en-us/sql/database-engine/sql-server-business-continuity-dr

• Windows Deployment Services (Optional, WDS is not always used):
  https://docs.microsoft.com/en-us/previous-versions/windows/it-pro/windows-server-2012-r2-and-2012/hh831764(v=ws.11)#configuring-the-wds-role-for-high-availability