This article presents a systematic and an efficient synthesis technique for designing single-band and dual-band waveguide (WG) filters with transmission zeros (TZs). The proposed electro-magnetic (EM)-based synthesis technique directly results in a filter design with an RF performance that is in excellent agreement with the ideal filter performance, thus significantly reducing the post fine optimization effort. Furthermore, the proposed technique also reduces the EM simulation resources required for the filter synthesis. The synthesis technique is lucidly explained by designing a symmetrical 6th-order WG filter with four TZs, a 9th-order filter with three asymmetric TZs and a 6th-order dual-band filter. To the best of the author’s knowledge, this is the first filter synthesis technique, which can be adopted to design WG filters, including TZs with minimum or no post fine optimization.