Secure communication is a necessity. However, encryption is commonly only applied to the upper layers of the protocol stack. This exposes network information to eavesdroppers, including the channel’s type, data rate, protocol, and routing information. This may be solved by encrypting the physical layer, thereby securing all subsequent layers. In order for this method to be practical, the encryption must be quick, preserve bandwidth, and must also deal with the issues of noise mitigation and synchronization. In this paper, we present the Vernam Physical Signal Cipher (VPSC): a novel cipher which can encrypt the harmonic composition of any analog waveform. The VPSC accomplished this by applying a modified Vernam cipher to the signal’s frequency magnitudes and phases. This approach is fast and preserves the signal’s bandwidth. In the paper, we offer methods for noise mitigation and synchronization, and evaluate the VPSC over a noisy wireless channel with multi-path propagation interference.