Mount Tsukuba Shrine sits at the foot of the mountain, close to the hiking paths and cable car. It is a good place to start or end a climb, with a huge bell, carved details in Nikko style, and the steady movement of walkers heading up toward the twin peaks.
The shrine gives Mount Tsukuba a cultural anchor, not just a trailhead. If you are taking the cable car, leave enough time to look around before joining the queue.