A method and apparatus for performing channel estimation using time-frequency localized pilots and de-noising techniques are disclosed. A transmitter sends pilot symbols which are localized in a joint time-frequency domain to a receiver for channel estimation. The receiver receives the pilot symbols and performs a time-frequency analysis, such as a discrete Gabor transform (DGT), to transform the received pilot symbols to a joint time-frequency domain. The receiver applies a de-noising technique, such as masking, to separate the pilot symbols from the embedded noise in the joint time-frequency domain. The receiver performs a time-frequency synthesis, such as an inverse discrete Gabor transform (IDGT), to generate a noise-removed pilot symbols in a time domain. The noise left after de-noising is only that part that overlaps with the pilot symbols in the joint time-frequency domain. The receiver then performs channel estimation with the noise-removed pilot symbols.