Wind farms (WFs) are increasingly connected to high-voltage (HV) grids, for which pilot protection—including differential protection and directional comparison blocking pilot protection (DCBPP)—is normally deployed as the primary relaying scheme. Despite extensive research into differential protection, the possible effects of WFs on DCBPP have not been studied to date. This paper unveils a serious defect associated with DCBPP that utilizes the superimposed component-based directional element (SCBDE) as the supervisory element. It is shown that for HV lines emanating from doubly fed induction generators (DFIGs)-based WFs, the positive-sequence SCBDE may provide misleading indications of fault directions during balanced faults, consequently causing the malfunction of DCBPP when faults are located inside protected lines. To secure the protection of lines during such problematic conditions, this paper also proposes a novel pilot protection scheme by applying the dynamic time warping (DTW) algorithm. The main idea behind the proposed scheme is to differentiate internal faults from external faults directly depending on the dissimilarity degree of current sampling sequences at two ends. Taking advantage of the distinctive waveshape properties of DFIG fault currents under crowbarred states, the proposed scheme can operate for internal faults at a high speed. In the meantime, the monotonicity and continuity attributes of the DTW algorithm enable the proposed scheme to be independent of a strictly identical sampling frequency and exhibit strong tolerance against synchronization errors and data packet loss. A thorough performance evaluation under various balanced faulty conditions corroborates the efficacy of the proposed scheme.