A base sequence determination apparatus includes (1) a mobility correction unit that outputs a mobility correction signal obtained by mobility correction of a time-series signal of a wavelength spectrum corresponding to each base, (2) a deconvolution unit that executes processes for calculating a deconvoluted signal of the mobility correction signal respectively for a plurality of parameter candidates of point spread function, calculating variance of peak intervals for the calculated deconvoluted signal, specifying a parameter of the point spread function using the calculated variance, and outputting the deconvoluted signal corresponding to the point spread function having the specified parameter as an updated deconvoluted signal, (3) a peak extracting unit that extracts a peak waveform from the updated deconvoluted signal and outputs an updated peak-extracted signal, and (4) a sequence specifying unit that inputs the updated peak-extracted signal and determines a base sequence.