This is done on Windows the same way you do on Linux.
ONE: Make a script in JavaScript to manage the task. This can be done in other languages if you prefer. This is a JavaScript script to rotate logs.
use admin
db.runCommand( { logRotate : 1 } )
TWO: Create a task in Task Scheduler to run the script. This can be done with the GUI, the API, or in XML. I usually set it up in the GUI and export the XML to allow parameterization of the database server, password, port, and user.
THREE: Include the execution of the script in the task
$MONGO_HOME/Mongo localhost:27017 -u myMongoServiceAccount -p somepassword LogRotate.js
The same concept can be applied to index management, gathering database stats, or managing stale locks.