Your usual run-of-the-mill Axis victory (Nazi Germany beats the USSR and an Allied landing doesn't happen or is beaten back, but Japan is still defeated by the Allies) could have the effect of delaying the emergence of proper high-speed rail (proper high speed rail in this case being a grade-separated system allowing speeds of at least 250 km/h, as per the European Union Directive's 98/48/EC's definition of category 1 high speed rail). A Japan that sees its allies Germany and Italy still alive and kicking is more likely to fight to the bitter end than in OTL, perhaps forcing more atomic bombings and a ground invasion of the Home Islands itself. The result being that Japan emerges from the war even more damaged and weakened than in OTL. Add in the Allies being focused on a more intense and expensive Cold War against Germany, and being less enthusiastic about funding the rebuilding of a former Axis power when it's farther the frontline of this Cold War than the OTL one, and when the other major Axis power is still a threat and now a superpower, and you could have Japan being in no economic or developmental position to build the Shinkansen by the 1960s.
The Shinkansen was a significant breakthrough for high-speed rail since it proved that grade-separation was viable, made a significant difference in average speed and time saved when they didn't share the line with slower trains, and that trains weren't an archaic form of transportation that was naturally and inevitably being superseded by cars and planes; they could still have a major place in intercity transport. It was the stated inspiration for high-speed systems in European countries, like the TGV, the ICE, and the Intercity 125/225, and even the increasing of train speeds in North America. Without it, the whole idea of high-speed rail could remain stuck in its interwar and postwar entropy for a longer time.
Nazi-ruled Europe, meanwhile, would still be touting the rapidly expanding Autobahn system and the auto industry as a source of national pride, and cars themselves as status symbols and something the average person would have the luxury of owning because of the state's prosperity and whatnot (the Volkswagen Beetle, the People's Car, was heavily featured in Nazi propaganda of the time), creating a car culture perhaps more comparable to our US in the second half of the 20th century than anything Europe has seen in OTL. Thus, heavy reliance on freeways and personal cars would have a similar effect on passenger rail travel as it did in the OTL US. While Nazi Germany did plan to build a grade-separated railway system for routes between major European cities (the ridiculously huge Breitspurbahn trains), from what few concept drawings I've seen those trains, they don't exactly look like trains designed to hit 250 km/h. The majority of Breitspurbahn locomotive designs seemed to be steam or diesel powered, and in OTL no steam locomotive has come close to hitting 250 km/h, and the fastest diesel locomotive (the Intercity 125) could only just barely manage that in a test run. The Breitspurbahn trains would probably be fast, but not the definition of high-speed kind of fast. Of course, this is assuming the project could even get off the ground, far from a guarantee given how uneconomically huge those trains were and the entropy and prestige loss that the rail system would likely suffer under car culture.
Still though, like the internet, the airline industry, and WMDs, this seems like an idea that, with an after-1900 PoD, will inevitably happen within the century (barring a civilization-ending apocalypse or something). The US has still gone through the Interurban Era, which, while it eventually ended, came pretty close to paving the way for proper high speed rail, and was a testbed for several of its key features (many lines were grade-separated, some sought to reduce or eliminate the use of grade crossings on the route, and nearly all used electric traction for the benefits in acceleration and speed it offered). The Northeast Corridor is still all too convenient a location for fast rail travel for people to ignore, and Britain would inevitably need to upgrade is then-archaic railway infrastructure sooner or later. Even in the year 1900, air-line railroads (relatively flat and straight railroads that deliberately chose a shorter and faster route over an easier route), lines dedicated to fast traffic, and the common designers' goal of making faster locomotives were not a new concept. As long as trains exist and are used to carry people, people will always have the idea, and make the effort, to make them move faster.
Proper high-speed rail can be delayed, but with a PoD of 1900, I think it would inevitably happen within the 20th century. Even if it can't be started in Japan, it will start somewhere, whether in the US, the UK, or another one of their allies.