Varenna to Last Supper

If you take the 7:37 a.m. regional train departing Varenna-Esino station, it arrives to Milano Centrale around 8:38. From there, you can catch a taxi out the side of the station (probably easiest), or go downstairs to the Metro and take line 2 (green) for 5 stops to Cadorna station, then walk 10 minutes to Santa Maria della Grazie. If you have Rick's book, maps and other info in the Milan chapter will also help you visualize.

You can buy train tickets either in Milan on your way out toward Varenna, or at the Barilott Bar/Tabac in Varenna (not at the station), or at www.trenitalia.com. These either need to be validated in a machine in the station, or a purchased for a specific time frame (but not seat assignment), depending on how you buy.

thanks so much -- can you tell me if the subway is easy to navigate?

Yikes! If you get into Milan Centrale at 8:38 a.m. and your tour is for 9:30 a.m., I would definitely take the taxi, since you only have 40 minutes.
When we went to The Last Supper several years ago, we took the subway, but then when we got off, we had to figure out the location of the entrance to The Last Supper. And even then, we didn't realize we needed to pick up our tickets (next door to where we were waiting). I had booked online and didn't realize the paper I printed was NOT the ticket. Luckily, we got there early to figure it all out.

yes -- i'm told that we need to be there no later than 9:10 to confirm the reservation and pick up the tickets. Would a taxi give us that time?

You're kinda pushing it here--if anything unanticipated happens (unanticipated, on Italian trainsy?), you probably won't see Last Supper. If you're ok with that possibility, fine.
If you're not ok with that, can you sleep in Milan night before? That's what we did on a previous trip, b/c seeing Last Supper was important to me.

There are also trains at 5:37, 6:23, and 6:39. Those will give you plenty of time to get there.

There are also trains that leave Varenna earlier than the one that Laura mentioned, beginning at 5:37. If you feel that is not enough time, you can take an earlier one to be safe.