The temperature-size rule (TSR) states that ectotherms mature at smaller adult body size in warmer conditions. Such a rule may have the potential to explain size response of fossil organisms to past temperature variations, but its validity in deep time has been seldom tested. The generality of this rule was investigated here by compiling data documenting the size record of three conodont genera (Palmatolepis, Ancyrodella and Polygnathus) at different spatial and temporal scales during the Late Frasnian and the Famennian, characterized by short- and long-term temperature variations. Statistical models were used to investigate the relationship between conodont size and oxygen isotope values, considered as paleotemperature proxies. Comparison of evolutionary models further allowed to test alternative modes of size variation such as stasis or punctuation. The TSR was not validated as a general rule explaining size variation in these fossil records, being only observed as a large-scale geographic trend during a time-slice. The only strong support for temperature being the driver of temporal variations was found regarding the size of Palmatolepis during the Kellwasser period, but the relationship was reverse to the expectation of the TSR. The absence of general TSR pattern is probably due to the interference of many other factors (demography and mortality patterns, temperature tolerance, size reduction due to stress) whose relative importance may depend on the time interval and the genus considered. Rather than a correlation with environmental proxies, evolutionary models suggested the occurrence of a synchronous shift in Palmatolepis size around 369 Ma (Palmatolepis termini conodont Zone) in several outcrops, raising questions about the environmental forcing beyond this shift. Departures from the expected TSR may thus provide relevant insights into the complex interplay of physical, tectonic and eco-evolutionary processes impacting size evolution in deep time.