The boundary layer plays a vital role in governing the local atmospheric dynamics and meteorology, including the vertical transport of moisture, momentum, energy, and air pollutants. Hence, accurate parameterization of the boundary layer processes is essential in atmospheric models such as the regional climate models (RCMs). However, evaluations of different boundary layer schemes within the Weather Research and Forecasting (WRF) model remain nearly non-existing over complex terrains of the Himalayan region. In this regard, six different planetary boundary layer (PBL) schemes: Yonsei University (YSU), Mellor-Yamada-Nakanishi-Niino level 3 (MYNN3), Shin-Hong Scale-aware (SHSS), Mellor-Yamada-Janjić (MYJ), Asymmetric Convective Model version 2 (ACM2), and Quasi Normal Scale Elimination (QNSE) in the WRF model have been evaluated against observations during the Ganges Valley Aerosol Experiment (GVAX). The evaluation is carried out for clear-sky conditions during spring (March 22–27, 2012) against surface-based, balloon-borne, and radar wind profiler (RWP) observations. The MYJ, YSU, and SHSS performed well in simulating the temperature and specific humidity, whereas the ACM2 (MYNN3) shows lower (higher) bias in T2 and higher (lower) bias in Q2. Model performance is limited in reproducing wind field (r ∼ 0.3) with different PBL schemes over this region. Model performance is seen to vary significantly with the choice of PBL schemes; nevertheless, all schemes could typically capture the daytime maxima in boundary layer height with some overestimation. The competing effects of synoptic versus local circulation were found to control the boundary layer evolution over the Himalayas, affecting the model performance. The model better reproduced the boundary layer evolution during strong surface flow regimes, while a prominent nocturnal peak in boundary layer height is observed during the weak mean flow conditions associated with topography-induced local circulations. The model performance is limited for reproducing such mountain meteorological features in contrast to the homogeneous terrains where such nocturnal peaks are absent. This study may serve as a reference for selecting a suitable PBL scheme for regional climate modeling studies in the future.