This study examined the emissions of nanoparticles and hazardous air pollutants (HAPs) by 3D printer operations and evaluated nanoparticle deposition behavior using a prediction model. Nanoparticles and HAPs were sampled at the Inha University 3D printing center with five fused filament fabrication (FFF)-type 3D printers. The number size distribution of the nanoparticles exhibited a bimodal distribution with dominant peaks over a large size range between 70 and 100 nm and a smaller size range between 10 and 20 nm. With increasing 3D printer operation, the number concentration of 10 nm particles increased, and the final number concentration was 3.6 times higher than that of the background concentration. Nanoparticle formation and agglomeration were characterized by transmission electron microscopy (TEM) and scanning electron microscopy (SEM). Model calculations revealed that a large number of nanoparticles between 10 and 30 nm in size are deposited in the lower human respiratory tract (generation number: 16–22). A total of 14 HAPs species were detected, among which hexane, acrylonitrile, and benzene concentrations were the highest.