We study the nonsteady Stokes flow in a thin tube structure composed by two thin rectangles with lateral elastic boundaries which are connected by a domain with rigid boundaries. After a variational approach of the problem which gives us existence, uniqueness, regularity results, and some a priori estimates, we construct an asymptotic solution. The existence of a junction region between the two rectangles imposes to consider, as part of the asymptotic solution, some boundary layer correctors that correspond to this region. We present and solve the problems for all the terms of the asymptotic expansion. For two different cases, we describe the order of steps of the algorithm of solving the problem and we construct the main term of the asymptotic expansion. By means of the a priori estimates, we justify our asymptotic construction, by obtaining a small error between the exact and the asymptotic solutions.