Yes, you can use the Japan Rail (JR) Pass to travel from Tokyo to Nara, but the journey typically requires a transfer. First, you take the Tokaido Shinkansen from Tokyo Station to Shin-Osaka or Kyoto Station. While the JR Pass covers the "Hikari" and "Kodama" trains for free, you must pay a special supplemental fee if you wish to use the faster "Nozomi" or "Mizuho" trains. Once you arrive at Kyoto Station, you transfer to the JR Nara Line for a direct local or rapid train to JR Nara Station. The entire trip is fully covered by the JR Pass as long as you use JR-operated lines. Note that JR Nara Station is about a 15-minute walk from the main park and deer area; the private Kintetsu Nara Station is closer, but your JR Pass is not valid on Kintetsu lines, so sticking to the JR Nara Line is the most cost-effective way for pass holders to visit the historic city.