The ever-increasing demand for private and sensitive data transmission over wireless networks has made security a crucial concern in the current and future large-scale, dynamic, and heterogeneous wireless communication systems. To address this challenge, wireless researchers have tried hard to continuously analyze the jamming threats and come up with improved countermeausres. In this research, we have analyzed the jamming-vulnerabilities of the leading multi-carrier communication systems, Orthogonal Frequency Division Multiplexing (OFDM) and Single-Carrier Frequency Division Multiple Access (SC-FDMA). In order to lay the necessary theoretical groundwork, first we derived the analytical BER expressions for BPSK/QPSK and analytical upper and lower bounds for 16-QAM for OFDMA and SC-FDMA using Pilot Symbol Assisted Channel Estimation (PSACE) techniques in Rayleigh slow-fading channel that takes into account channel estimation error as well as pilot-jamming effect. From there we advanced to propose more novel attacks on the Cyclic Prefix (CP) of SC-FDMA. The associated countermeasures developed prove to be very effective to restore the system. We are first to consider the effect of frequency-selectivity and fading correlation of channel on the achievable rates of the legitimate system under pilot-spoofing attack. With respect to jamming mitigation techniques, our approaches are more focused on Anti-Jamming (AJ) techniques rather than Low Probability of Intercept (LPI) methods. The Channel State Information (CSI) of the two transceivers and the CSI between the jammer and the target play critical roles in ensuring the effectiveness of jamming and nulling attacks. Although current literature is rich with different channel estimation techniques between two legitimate transceivers, it does not have much to offer in the area of channel estimation from jammer's perspective. In this dissertation, we have proposed novel, computationally simple, deterministic, and optimal blind channel estimation techniques for PSK-OFDM as well as QAM-OFDM that estimate the jammer channel to the target precisely in high Signal-to-Noise (SNR) environment from a single OFDM symbol and thus perform well in mobile radio channel. We have also presented the feasibility analysis of estimating transceiver channel from jammer's perspective at the transmitter as well as receiver side of the underlying OFDM system. / Ph. D.