Test-retest reliability, or reproducibility of results over time, is poorly established for functional brain connectivity (fcMRI) during painful stimulation. As reliability informs the validity of research findings, it is imperative to examine, especially given recent emphasis on using functional neuroimaging as a tool for biomarker development. Although proposed pain neural signatures have been derived using complex, multivariate algorithms, even the reliability of less complex fcMRI findings has yet to be reported. The present study examined the test-retest reliability for fcMRI of pain-related brain regions, as well as self-reported pain [via visual analogue scales (VASs)]. Thirty-two healthy individuals completed three consecutive fMRI runs of a thermal pain task. Functional connectivity analyses were completed on pain-related brain regions. Intraclass correlations (ICC) were conducted on fcMRI values and VAS scores across the fMRI runs. ICC coefficients for fcMRI values varied widely (range = −.174–.766), with fcMRI between right nucleus accumbens and medial prefrontal cortex showing the highest reliability (range = .649–.766). ICC coefficients for VAS scores ranged from .906–.947. Overall, self-reported pain was more reliable than fcMRI data. These results highlight that fMRI findings might be less reliable than inherently assumed, and have implications for future studies proposing pain markers.