Though standing computer workstations are now a popular option for workplace intervention, there is currently not a specific set of ergonomic guidelines to set up standing computer workstations. This study utilized a 3-hour psychophysical protocol to examine how user’s preference affects their workstation setup based on their perceived comfort level while performing standing computer work. We found that users preferred having their keyboard more distant away to their body when they were standing compared to if they were sitting. Users also preferred to set their table height lower to their elbow height and had their monitor lower compared to their eye level. Subsequent protocol evaluation and trend analysis showed that our protocol was effective and consistent while allowing users freely adjust their workstation to find their preferred setup that they felt they were most comfortable with. We see our results as the first step towards making recommendations to establish ergonomic guidelines for standing computer workstation setup.