In this work, we develop a new design method based on fast Fourier transform (FFT) for implementing zone plates (ZPs) with bifocal focusing profiles. We show that the FFT of the governing binary sequence provides a discrete sequence of the same length, which indicates the location of the main foci at the ZP focusing profile. Then, using reverse engineering and establishing a target focusing profile, we are capable of generating a binary sequence that provides a ZP with the desired focusing profile. We show that this design method, based on the inverse fast Fourier transform (IFFT), is very flexible and powerful and allows to tailor the design of bifocal ZPs to achieve focusing profiles with the desired foci locations and resolutions. The key advantage of our design algorithm, compared to other alternatives presented in previous works, is that our method provides bifocal focusing profiles with an absolute control of the foci locations. Moreover, although we analyze the performance of this novel design algorithm for underwater ultrasonics, it can also be successfully extended to different fields of physics, such as optics or microwaves, where ZPs are widely employed.