This paper proposes a speech enhancement algorithm for pathological voices using a time-frequency trajectory excitation (TFTE) modeling. The TFTE model has a capability of delicately controlling the periodic and non-periodic excitation components by taking a single pitch based decomposition process. By investigating the difference of frequency characteristics between pathological and normal voices, this paper proposes an enhancement algorithm which can efficiently reduce the breathiness of the pathological voice while maintaining the identity of the speaker. Subjective test results are presented to verify the effectiveness of the proposed algorithm.