Characterizing the thermal preference of fish is important in conservation, environmental and evolutionary physiology and can be determined using a shuttle box system. Initial tank acclimation and trial lengths are important considerations in experimental design, yet systematic studies of these factors are missing. Three different behavioral assay experimental designs were tested to determine the effect of tank acclimation and trial length (hours of tank acclimation:behavioral trial: 12:12, 0:12, 2:2) on the temperature preference of juvenile lake whitefish (Coregonus clupeaformis), using a shuttle box. Average temperature preferences for the 12 h:12 h, 0 h:12 h, 2 h:2 h experimental designs were 16.10±1.07°C, 16.02±1.56°C and 16.12±1.59°C respectively, with no significant differences between experimental designs (P=0.9337). Ultimately, length of acclimation time and trial length had no significant effect on thermal preference.