According to All About Birds, "When males court females, they fan or flick open their wings and tail, hop up and down, and pick up pieces of nest material or moss; females seem to prefer males that show more white in the tail." Juncos are generally monogamous.

Juncos are typically ground nesters, hiding their nest under overhanging vegetation or against a protective rock outcropping or other upright structure or even underneath buildings. Occasionally they will nest above ground, seldom more than 45' on horizontal branches or sometimes in flower pots or on window ledges. New nests are built every year, usually in the same territory. While the female incubates her three to five eggs without the male's help, the two will work together to bring food to the babies on the average of eight times per hour. The young can fledge at three weeks, attended by their father while the mother prepares for a second brood. As is typical of ground nesting birds, they can run long before being able to fly.