The boundary effects on the current-voltage characteristics in two-dimensional arrays of resistively shunted Josephson junctions are examined. In particular, we consider both the conventional boundary conditions (CBC) and the fluctuating twist boundary conditions (FTBC), and make comparison of the obtained results. It is observed that the CBC, which have been widely adopted in existing simulations, may give a problem in scaling, arising from rather large boundary effects; the FTBC in general turn out to be effective in reducing the finite-size effects, yielding results with good scaling behavior. To resolve the discrepancy between the two boundary conditions, we propose that the proper scaling in the CBC should be performed with the boundary data discarded: This is shown to give results which indeed scale well and are the same as those from the FTBC.