This work compares the coded aperture imaging performance of thermionic filament and carbon nanotube (CNT) field emitter-based electron sources in cycloidal-coded aperture mass spectrometers. The use of spatially coded apertures in mass spectrometry enables miniaturization by improving throughput without sacrificing resolution. CNT-based electron ionization sources for mass spectrometers provide several potential benefits over conventional thermionic emitters, including low voltage and low power consumption, room temperature operation, long lifetime, and ability to emit electrons in a pulsed mode. However, spatiotemporal variation in electron emission from CNTs is a major disadvantage. In this study, electron emission stability and spatiotemporal stability of the coded aperture image were compared for coded aperture cycloidal mass analyzers with either a CNT-based ion source or a thermionic filament-based ion source. We found that the thermionic filament-based ion source produced a significantly more stable coded aperture image than the CNT based ion source. The aperture image fluctuations in the CNT-based source are likely a result of adsorption and desorption of molecules on the CNT surface that cause local work function changes and induce spatiotemporal variation in electron emission and subsequent ion generation.