Kyoto is in the middle of the Kansai region, which means nearly every important historic city in western Japan is within day-trip range by train. Nara, an hour away on the Kintetsu line, was the capital before Kyoto and is home to the colossal bronze Buddha at Tōdai-ji and a deer park where the tame deer bow to visitors for biscuits. Osaka, 15 minutes on the shinkansen, is Japan's great food city and a total change of pace from Kyoto. Himeji, an hour the other way, has the country's most spectacular surviving castle. Further afield, Hiroshima and the shrine island of Miyajima are reachable on the shinkansen (about 100 minutes) for a long but entirely feasible day. And the quiet castle town of Hikone and the pine-covered sandbar of Amanohashidate on the Sea of Japan coast are pleasant alternatives to the better-known sights.
Closer in, several worthwhile half-day escapes are really single sights rather than whole towns: the Phoenix Hall at Byōdō-in in the tea town of Uji, the riverside Kifune Shrine and its lantern-lit steps in the northern mountains, and the moss gardens of Sanzen-in in the village of Ōhara.