We consider the problem of designing waveforms for mitigating single tone jamming (STJ) signals with an estimated jamming frequency in time-hopping spread spectrum (TH SS) systems. The proposed design of waveforms optimizes the anti-jamming (AJ) performance of TH SS systems by minimizing the correlation between the template and STJ signals, in which the problem of waveform optimization is simplified by employing a finite number of rectangular pulses. The simplification eventually makes the design of waveforms be converted into a problem of finding eigenvalues and eigenvectors of a matrix. Simulation results show that the waveforms designed by the proposed scheme provide us with performance superior not only to the conventional waveforms but also to the clipper receiver in the mitigation of STJ. The waveforms from the proposed design also exhibit a desirable AJ capability even when the estimated frequency of the STJ is not perfect.