Flight from Mlano-MXP to Rome-FCO -

At the risk of sounding dumb, why not just book a flight to Rome from your origin point ( wherever that is)?

Separate bookings are a hazard due to the previous flight having to be on time and what lines/delays you may have, if you need to go through passport control at MXP.

If arriving on an intercontinental flight, I would book nothing earlier than noon as a separate onward flight to Rome, especially if you have checked luggage

The big question is where you will be coming from to MXP. However, even with an intra EU flight, an hour and a half is cutting it too close. I’m pretty sure I’ve read about Ryan being very inflexible about how much before take-off you need to be on board.

Have you checked out trains?

I am sorry, but I do not see any direct flights from MXP to FCO. All the choices require at least one connection. Vueling connects via Barcelona, Swiss via Zurich, Ryanair only goes to cities in the south, like Palermo and Catania. They all take over 4 hours.

Why don't you take the train. Malpensa Express train to Milano Centrale, then Freccia train to Rome Termini. You can probably make it there by 2 pm. A lot more relaxing than flying all over Europe to go 500 km.

Edit - Further out, in April, I am seeing a single Alitalia flight at 11:10 am. If that is running on your travel date, its a possibility. But it arrives at FCO at 12:25, and by the the time you get to Rome center, (assume that is where you are going) , it will be 2 pm, same time as the train.

As others have said, take the train. I'm off to Rome tomorrow for the Six Nations however flights to Rome were ridiculously inflated so instead we booked significantly cheaper tickets to Milan and taking the train to Rome Termini. It takes just under three hours which would likely to be the same amount of time flying when taking into account the checking in times etc and for me it's more comfortable and relaxing. It also takes us slap bang in the middle of Rome and with our hotel a five minute walk away we're ready to explore within 15 minutes of arrival.

Indeed, the train for the win in this situation!

Have you read this board's host's general air tips? Start here:
https://www.ricksteves.com/travel-tips/transportation/booking-flights

I will say that we once flew to Milan because there was such a surplus of flights there during the past Worlds Fair event. Airlines couldn't get rid of all their seats. But in general, Rome is such a busy airport that you should fly directly there. Unless you have things you want to do in Milan (or in one of our trips, Venice), I can't recommend your plan.

Have you already bought the tickets to Milan? It would have helped if you gave your nationality and departure country - That's because your OP shows no preparation for immigration and customs delays. If this is your first trip to Europe, please say so. Our host's travel books specialize in that kind of advice.

You are out of luck. Unless there has been a change in the last few weeks, all airlines have stopped flying from Milan MXP to Rome. The last one was EasyJet which discontinued their flights recently.
The most logical option would be to fly directly to Rome from the origin Airport you are flying from. If that is impossible or too costly, then the train is the fastest option. You can take the Malpensa Express train to Milano Centrale (about 50 min) then the Freccia Rossa to Rome Termini (2h45m). Even a non stop flight couldn’t do better once you take into consideration, check in, wait times, security, boarding, flight time, transfer from Fiumicino airport to Rome.