An apparatus and method for bio-particle detection are provided. The apparatus for bio-particle detection includes: a bio-particle detection chip including a substrate having a plurality of through-hole groups, each through-hole group of the plurality of through-hole groups including through-holes which pass through the substrate from a first surface of the substrate toward an second surface of the substrate opposite to the first surface, and which are configured to accommodate a sample solution loaded therein; and a processor configured to determine a number of through-holes, among the through holes of at least one through-hole group of the plurality of through-hole groups, having a target material encapsulated therein, based on at least one of an electrical signal and an optical signal corresponding to the through-holes of the at least one through-hole group, and to estimate a concentration of the target material based on the determined number.