Frequency Hopping Spread Spectrum (FHSS) system is often deployed to protect wireless communication from jamming or to preclude undesired reception of the signal. Such themes can only be achieved if the jammer or undesired receiver does not have the knowledge of the spreading code. For this reason, unencrypted M-sequences are a deficient choice for the spreading code when a high level of security is required. The primary objective of this paper is to analyze vulnerability of linear feedback shift register (LFSRs) codes. Then, a new method based on encryption algorithm applied over spreading codes, named hidden frequency hopping is proposed to improve the security of FHSS. The proposed encryption security algorithm is highly reliable, and can be applied to all existing data communication systems based on spread spectrum techniques. Since the multi-user detection is an inherent characteristic for FHSS, the multi-user interference must be studied carefully. Hence, a new method called optimum pair “key-input” selection is proposed which reduces interference below the desired constant threshold.