Diltiazem was determined at the sub-nanomolar level for the first time by a new technique, involving fast Fourier continuous cyclic voltammetry in a flow-injection system. The best performance was achieved with the basic parameters being set at pH value of 2.0, scan rate value of 35 V/s, accumulation potential of 300 mV and accumulation time of 0.8 s. This paper additionally introduces a special computer based numerical method for the calculation of the analyte signal and the noise reduction. Concerning the electrode response calculations were carried out according to the partial and total charge exchanges on the electrode surface after subtraction of background current from that of noise. Furthermore, to obtain a sensitive determination, the currents integration range included all potential scan ranges, even oxidation and reduction of the Au surface electrode, during the measurements. In general, the potential waveform includes the potential steps for cleaning, accumulation and the step of the potential ramp of the analyte. This potential waveform was applied to an Au disk microelectrode in a continuous way. Finally, the method was found to be linear for the concentration range of 1-41450 pg/ml (r = 0.9986), while showing a limit of detection and quantitation of 0.29 and 1 pg/ml, respectively.