The brown treesnake (Boiga irregularis, or BTS), a costly invasive species, has been the subject of intensive research on Guam over the past two decades. The behavior and habitat use of hatchling and juvenile snakes, however, remain largely unknown. We used a long-term dataset of BTS captures (N = 2,415) and a dataset resulting from intensive sampling within and immediately around a 5-ha fenced population (N = 2,541) to examine habitat use of BTS. Small snakes were almost exclusively arboreal and that they appeared to prefer tangantangan (Leucaena leucocephala) habitats. In contrast, large snakes used arboreal and terrestrial habitats in roughly equal proportion, and were less frequently found in tangantangan. Among snakes found in trees, there were no clear size-based preferences for certain heights above ground, nor for size-based choice of perch diameters. We discuss these results as they relate to management and interdiction implications for brown treesnakes on Guam and in potential incipient populations on other islands.