Literally 'newly-built shrine', 'young shrine'. It generally means a shrine dedicated to the 'divided spirit' (bunrei) of a kami. Wakamiya shrines may be established to console the bunrei of a deity enshrined in a main shrine, to revere the offspring (mi-ko-gami), a subset of the kenzoku or retinue of a main kami, or to console a vengeful spirit, goryo.
See also Wakamiya jinja.
A Popular Dictionary of Shinto. Brian Bocking.