This paper presents an efficient pitch estimation algorithm for noisy speech signal using ensemble empirical mode decomposition (EEMD) based time domain filtering. The dominant harmonic of noisy speech is enhanced to make pitch period more prominent. The normalized autocorrelation function (NACF) of the modified signal is then decomposed into time varying subband signals using EEMD. In contrast to the ordinary EMD, it does not introduce any mode mixing during decomposition. The subbands containing pitch component are selected and separated yielding partially reconstructed signal. The pitch period is determined from thus separated signals. The experimental results show that the proposed algorithm performs better compared to other recently reported algorithms in noisy environment.