Invasive sea lamprey (Petromyzon marinus) in the Laurentian Great Lakes have negatively impacted ecologically and economically important fishes for nearly a century. To mitigate these effects, the lampricide 3-trifluoromethyl-4-nitrophenol (TFM) is applied annually on a rotating basis to selected Great Lakes tributaries to kill larval lamprey before they become juveniles, out-migrate to the lakes, and parasitize other fishes. It has been hypothesized that larval size (e.g., mass, length) may affect survival time in response to TFM. To test this hypothesis, we conducted an experiment with 8611 larvae across four temporal replicates, in which TFM concentrations equivalent to those used in present-day stream treatments were applied for up to 18 h. When examining the survival times of larval lamprey exposed to TFM, we found a significant, positive relationship between length, mass, toxicity, and their interactions. For every 1 mm increase in total length, a corresponding increase by 1 g of mass reduced survival time by 0.4315 min [95 % CI: 0.5283–0.2992] and vice versa (i.e., the significant interaction between length and mass revealed that as larvae increase in mass, the survival benefit to being longer decreases, and vice versa). The changes in total length and mass of larval sea lamprey stored in ethanol for 4 months was also quantified. The observation that five larvae survived well past the 12-hour time window of a typical TFM field treatment highlights the need for continuous monitoring and the development of new control strategies to ensure the continued effective management of this invasive species.