An apparatus for estimating an analyte concentration includes a spectrum acquisition device configured to obtain a plurality of in vivo spectra for training which are measured during a first interval, and obtain an in vivo spectrum for analyte concentration estimation which is measured during a second interval, and a processor configured to generate a plurality of candidate concentration estimation models by varying a number of principal components based on the plurality of in vivo spectra for training, obtain a plurality of residual vectors corresponding to the plurality of in vivo spectra for training by using the plurality of candidate concentration estimation models, select a candidate concentration estimation model, from among the plurality of candidate concentration estimation models, based on the plurality of residual vectors, and estimate the analyte concentration by using the selected candidate concentration estimation model and the in vivo spectrum for analyte concentration estimation.
