Having just visited Santa Fe and planned a trip to Lamy and ABQ on the side, here's my first hand advice having just cut my teeth on this precise issue...
COMING EAST
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If you'd like to spend a few hours visiting Albuquerque (perhaps get a bite for lunch, do some shopping, etc), definitely consider the
New Mexico RailRunner Express as a way to get from Albuquerque to Santa Fe. The RailRunner is a commuter train that runs multiple times per day between the two cities and is rather cheap at $7 a pop ($3 for students/seniors/disabled with ID). Assuming you arrive in Albuquerque on-time at 11:42 AM, the next RailRunner out departs Albuquerque on Saturdays at 2:38 PM, arriving in Santa Fe at 4:10 PM. On Sundays, it departs Albuquerque at 4:44 PM and arrives in Santa Fe at 6:16 PM. On Weekdays, the Railrunner departs Albuquerque at 4:18 PM, giving you roughly 4 and a half hours to tour Albuquerque. The Railrunner arrives in downtown Santa Fe at 6:00 PM.
If getting to Santa Fe as quickly as possible is your goal (and you don't care to see Albuquerque), take the Chief all of the way to Lamy, arriving at 1:17 PM. You have TWO connection options from there.
The first (and fastest) option is to book the connecting van shuttle from Lamy to Santa Fe, which is $20 per person, each way. They'll have you into Santa Fe by 2:00 PM or so. The van can be booked through Amtrak as part of your larger reservation, or it can be picked up in Lamy when you get off if you have cash on you. They will drop you off wherever you want to go in Santa Fe.
The second option is to take the
Santa Fe Southern Railway from Lamy to Downtown Santa Fe. The Santa Fe Southern connects with the Chief in both directions on Fridays (April-October) and Saturdays (year-round). The train to Santa Fe departs Lamy at 2:00 PM on Fridays (they will wait for a delayed Chief if they know you are coming, but it's best to make this clear when you make your reservation by phone). The train departs Lamy at 3:00 PM on Saturdays (sometimes they'll leave earlier if you're the only one riding), which means you'll have some time to relax in Lamy and have lunch (you'll need to bring your own though; there is a park with picnic benches, but not much else besides the train station and the train, which you are welcome to board early). The train arrives back in Santa Fe by 3:00 PM on Fridays and by 4:00 PM on Saturdays. The trip costs $32 each way/$27 for seniors (reservations are required via phone or on their website) and is provided in restored antique passenger cars dating from the 1920's. It's a scenic trip and they serve alcohol and refreshments on board and provide a narration as well.
HEADING WEST
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You have the three same options for going west: The RailRunner, the Van Shuttle, and the Santa Fe Southern.
The Railrunner departs the Santa Fe Depot at 11:33 AM on Weekdays and arrives in Albuquerque at 1:02 PM. On weekends, the RailRunner departs Santa Fe on Saturdays at 1:17 PM and arrives in Albuquerque at 2:54 PM. On Sundays, the Railrunner departs Santa Fe at 11:20 AM and arrives in Albuquerque at 12:56 PM. The Chief departs Albuquerque daily at 3:55 PM.
The Van will pick you up from wherever you are in Santa Fe and will meet the train in Lamy; the van driver will coordinate with you ahead of time, usually via cell phone.
The Santa Fe Southern departs from Santa Fe at 11:00 AM on Fridays (April-October) and at noon on Saturdays (year round), dropping you off in Lamy at 12:00 PM and 1:00 PM, respectively. The Chief departs Lamy at 2:24 PM.
NOTE: The Santa Fe Southern is completing track work (actually, it's been completed; they're waiting on FRA inspection to open the line in a week or two) and is not running trains until the end of June. If you're interested in that option, it's best to call them to confirm availability first. Their number is 505-989-8600.
ALSO NOTE: If the eastbound Chief is running grossly late, the Santa Fe Southern will wait as long as they can, but will eventually leave. If they leave before the Chief arrives, you can pay the Amtrak Van Shuttle $20 cash on the spot (no reservation required) for passage to Santa Fe.
Rafi