From Emperor of Japan: Meiji and His World, 1852–1912, by Donald Keene (Columbia U. Press, 2005), Kindle pp. 188-189:
Earlier in 1869 when Emperor Meiji was about to leave for his second visit to Tōkyō, the people of Kyōto had been informed that he would return to their city in April or May of the following year and would celebrate his Daijō-e [大嘗会 ‘great tasting meeting’ = Daijō-sai ‘great tasting ceremony’] there in the winter of that year. This announcement had quieted their anxiety, only for them to be informed in the spring of 1870 that the emperor’s return to Kyōto had been unavoidably delayed because of unsettled conditions in parts of the country and the pressure of state business. A year later, on May 15, 1871, it was announced that the Daijō-e would be performed in Tōkyō instead. On May 24 Major Counselor Tokudaiji Sanetsune was sent as a special envoy to Kyōto to report to the tomb of Emperor Kōmei [Meiji’s father] that conditions in the world and an increased burden of state duties had compelled the emperor to postpone his return to Kyōto. Tokudaiji also visited the empress dowager and informed her that the emperor’s return to Kyōto would be delayed for several years.
The emperor did not in fact return to Kyōto (except for brief visits) until 1877. At no point was it officially announced that the capital was now Tōkyō and not Kyōto. All the same, when Meiji at last returned to Kyōto, his journey was characterized as gyōkō [行幸 ‘go luck’], a going away from his residence, rather than as kankō [還幸 ‘return luck’], a return to his residence, the term used when he returned to Kyōto from Tōkyō in 1868. By 1877 Tōkyō was functionally the capital of Japan, not only because it was the seat of the emperor and all organs of the government, but also because the foreign legations were situated there. However, the government hesitated to make this official, perhaps fearing the reactions of the people of Kyōto. Meiji would be buried in Kyōto, and the coronation of his son, Emperor Taishō, would also take place there in 1915, suggesting the persistence of the belief that in certain respects anyway, Kyōto was still the capital. It might even be argued, in the absence of a proclamation to the contrary, that Kyōto remains to this day the capital of Japan.
This must have been a confusing time for early railway timetable makers. Nowadays, trains “ascend” toward Tokyo, but “descend” away from Tokyo. However, the Kyoto Railway Museum displays an old timetable (from the 1870s or 1880s) whereon “ascending” destinations include Osaka, Himeji, and Maibara to the south, while “descending” destinations include Kanazawa, Toyama, Niigata, and Ueno (in Tokyo) to the north.