The dynamics of highly flexible micro- and nano-filaments are important to a variety of biological, medical, and industrial problems. The filament configuration variation and cross-stream migration in a microchannel are affected by thermal fluctuations in addition to elastic and viscous forces. Here, hydrogel nano-filaments with small bending Young's moduli are utilized to elucidate the transitional behavior of elastic Brownian filaments in an oscillatory microchannel flow. A numerical model based on chain elastic dumbbells similar to the Rouse-Zimm model accounting for elastic, viscous, and random Brownian forces is proposed and implemented. In addition, a theoretical model to describe the average orientation-deformation tensor evolution for an ensemble of filaments in an oscillatory flow is proposed. The results are compared with the evolution observed in the experiments.