Study of species’ ecological niches through evolutionary history can elucidate speciation mechanisms, yet current comparative phylogenetic methods consistently overestimate niche evolution. Here we propose a method by which to characterize species’ fundamental ecological niches for comparative phylogenetic analysis using a bin-based approach that incorporates uncertainty in niche estimates. Simulation analysis using a traditional characterization method (median value calculated from species’ known occurrences) estimated a significantly higher rate of niche evolution than using our proposed method, and differences in rate estimates were consistent regardless of the number of simulated taxa in a phylogeny. We also demonstrate how to perform ancestral state reconstructions under the new coding system; reconstructions are performed for each bin individually, and ancestral fundamental niches inferred by smoothing each node’s reconstructions across all bins. Finally, we provide a worked empirical example of our method, investigating ecological niche evolution in 34 species of New World orioles (Icterus spp.). Ecological niches were generally conserved in the group, and only a few lineages appear to have experienced niche reduction and specialization.