The northern long‐eared bat (Myotis septentrionalis) is one of the bat species most affected by white‐nose syndrome. Population declines attributed to white‐nose syndrome contributed to the species’ listing as federally threatened under the 1973 Endangered Species Act. Although one of the most abundant Myotine bats in eastern North America prior to white‐nose syndrome, little is known about northern long‐eared bats in the upper Midwest, USA. We assessed the habitat associations of the northern long‐eared bats on a regional scale using occupancy models that accounted for uncertainty in nightly detection to provide needed information on the distribution as white‐nose syndrome has recently arrived in this area. We monitored bat activity using zero‐crossing frequency‐division bat detectors for 10–15 nights at 20 detector sites at each of 3 sampling areas in Michigan, USA, and 6 sampling areas in Wisconsin, USA, stratified by mesic and xeric habitat types. We constructed northern long‐eared bat nightly detection histories for our occupancy analysis using maximum likelihood estimates from 2 commercially‐available automated identification programs: Kaleidoscope and Echoclass. We sampled for a total of 2,174 detector‐nights. Both Kaleidoscope and Echoclass identified northern long‐eared bat passes on 110 detector‐nights, whereas on 1,968 detector‐nights neither program identified a northern long‐eared bat call. Only one program or the other identified northern long‐eared bat calls on 206 detector‐nights, indicating an overall agreement rate of 35% on nights when calls were detected. We analyzed these data using an occupancy analysis accounting for the potential for false positives to assess the relationship between northern long‐eared bat presence and habitat characteristics. Our analyses indicated that the probability of a false positive at a site was low (0.015; 95% CI 0.009–0.021), and detection probability, but not occupancy, declined from 2015 to 2016 for sites in Wisconsin sampled in both years. Occupancy was positively associated with distance into the forest interior (distance from nearest road).