Channel estimation is a challenging and timely issue for the 3rd Generation Partnership Project (3GPP) standardized low power wide-area network technology named narrowband Internet of Things (NB-IoT). Channel estimation is crucial to achieve extended radio coverage, energy efficiency, coherent detection, and channel equalization for signal repetition dominated NB-IoT uplink transmission. The NB-IoT inherits simplified baseband radio frequency processing, physical channels, reference signal structure, and numerology from existing Long Term Evolution (LTE) systems to save power and costs. Thus, channel estimation methods extensively employed in LTE systems may not be applied to the NB-IoT uplink systems. In this paper, efficient discrete cosine transform type-I (DCT-I)-based transform-domain channel estimation approaches are proposed by modifying the original definition of DCT-I. The proposed methods can mitigate the problems experienced in the discrete Fourier transform (DFT)-based channel estimation, such as signal aliasing error, and border effect. The proposed approaches improve channel estimation precision by reducing signal distortion from the high-frequency region in the time-domain when non-sample-spaced path delays exist in multipath fading channels. Signal aliasing error experienced from the virtual subcarriers is also minimized with the anticipated schemes. The proposed methods are applied on simple least squares (LS) estimates in time-domain to eliminate estimation noise. The viability of the proposed estimators is verified as compared to the conventional LS, DFT-based de-noising LS, and standard DCT-I based methods through extensive numerical simulations. Based on the numerical simulations, the proposed estimators show better mean square error and bit error rate performances than their competitors in extremely low coverage conditions.