SummaryThermally sensitive fluorescent indicators have been proposed to monitor temperature changes in microfluidic systems, mainly based on fluorescence intensity or lifetime. However, measuring temperature in a structured environment, such as biological tissue, presents additional challenges due to the chemical and structural complexity. Here, we investigate the potential for resolving temperature distributions within the volume of a single cell. Rhodamine B (RhB) dye was employed as a temperature indicator to compare fluorescence intensity‐ and lifetime‐based techniques. The relationship between the fluorescence lifetime and temperature was found to be highly dependent on the biological environment. The intensity‐based method allowed the temperature distribution to be mapped with partial success within the volume of a single cell. Under ideal circumstances, the temperature can be mapped pixel by pixel with a resolution better than ±0.3°C within the cell cytoplasm, but this accuracy was reduced to ±1.8°C by environmental variations. These results suggest that the fluorophore should be encapsulated and immobilized in the biological tissue in order to reduce the influence of environmental factors on temperature measurements at the cellular level.