We give a fully polynomial-time approximation scheme (FPTAS) to count the number of independent sets on almost every $Δ$-regular bipartite graph if $Δ\ge 53$. In the weighted case, for all sufficiently large integers $Δ$ and weight parameters $λ=\tildeΩ\left(\frac{1}Δ\right)$, we also obtain an FPTAS on almost every $Δ$-regular bipartite graph. Our technique is based on the recent work of Jenssen, Keevash and Perkins (SODA, 2019) and we also apply it to confirm an open question raised there: For all $q\ge 3$ and sufficiently large integers $Δ=Δ(q)$, there is an FPTAS to count the number of $q$-colorings on almost every $Δ$-regular bipartite graph.