If you fly, you have 4 options from BWI:
1.) MARC train: by far the best option for money & time. It only runs on the weekdays, and you have to catch a shuttle that runs every 10 minutes on the ground floor outside of BWI. You take it to the BWI Rail Station, where you can catch a MARC train going to Penn Station in Baltimore. The ticket costs less than 5 dollars, and the ride is 20 minutes to Penn Station. From there, you can either take a cab or the JHU Homewood-JHMI shuttle.
2.) Light rail: If you walk on the ground floor of BWI all the way around (away from Southwest), you will come to a rail that comes directly to BWI (no shuttling). The ticket machines are outside and the ticket costs $1.60, might need exact change. The length of the ride is HIGHLY VARIABLE. Depending on traffic (it cuts through parts of downtown!), you are looking at a ride anywhere from 30 min to an hour. Some of the light rails stop at Penn Station, SOME DO NOT. Always safer to get off at the University at Baltimore stop, which is 2-3 blocks from Penn Station. Again, from there, you can take the cab or JHU shuttle.
3.) Super Shuttle: On the ground floor of BWI, there are several Super Shuttle booths. For 19 dollars + x tip dollars, they will take you whereever you want in Baltimore. However, the wait for the shuttle can vary, up to a hour during peak periods, and the drive depends on how many passengers are on the shuttle.
4.) Cab. Most expensive. Baltimore cab drivers love to take the scenic route, and they upped the rates not too long ago.
If you take the train (or take light rail or MARC from BWI), you have 2 options from Penn Station
1.) Homewood-JHMI shuttle: On either side of Penn Station (outside), there are two shuttle stops. The North Charles stop is the Northbound shuttle, going to Homewood campus. The St. Paul stop is the Southbound shuttle, going to JHMI. The schedule is here:
http://www.parking.jhu.edu/shuttles_jhmi-homewood.html
Now those departure times are from Homewood (undergrad campus), add anywhere from 5-15 min to those times for arrival at Penn Station for pickup. Also note that some shuttles are marked as EXPRESS shuttles, and DO NOT stop at Penn Station. The ride takes about 8-15 min from Penn Station, depending on traffic.
2.) Cab. Price & time depends on traffic, if you pay more than 15 you got ripped.
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I've done every one of these modes of transportation, and they all work provided the situation fits. If you are brand new to Baltimore and if you are coming on interview day, I'd suggest cabbing it or using Super Shuttle (careful with shuttle), because timing the MARC and Light Rail is kind of hard with all the airport/Penn Station shuttling and stuff. If you have been to Baltimore and are familiar with the transportation system, and/or if time is not of the essence (ie if you aren't coming on interview day, but the night before), I would say MARC or Light Rail, preferably the former.