The head temple was founded in 1342 by the Zen master Kanzan Egen (関山慧玄, 1277–1360), third patriarch in the influential Ōtōkan lineage.

The present buildings were primarily built during the following 150 years (late 15th through early 17th century),[3] and today the gardens of Myōshin-ji are a nationally designated Place of Scenic Beauty and Historic Site.

[6] The complex is quite sprawling, and features a number of winding paths flanked by high walls, so it is easy to become disoriented when walking the grounds.

As is usual in Japanese temple construction, the main buildings are located on the axis that extends north from the south gate, in the south-west quadrant of the complex.

In addition to these main routes, there are a number of side paths which are all lined with sub-temples, generally each with a single entrance.

In the southeast corner of the square plot of the temple complex proper is the associated Hanazono High School, just across a small river.