The cosmogenic isotope 41Ca with a half-life of 99,000 years can, in principle, serve as a tracer for environmental processes at an age scale beyond the reach of 14C. With accelerator mass spectrometry, the ratio of 41Ca/Ca has been measured down to the 10−15 level in natural samples. A wide range of potential applications, such as the burial dating of bones and exposure dating of rocks, require measuring even smaller 41Ca/Ca ratios in the range of 10−16 to 10−15. Here we achieved this by employing the atom-trap trace analysis method in which individual 41Ca atoms are selectively captured in a magneto-optical trap and counted by detecting their fluorescence. We realized a precision of 12% on the 41Ca/Ca ratio at the level of 10−16 and achieved a detection limit at the level of 10−17, which is below the distribution of natural abundances. We verified the accuracy of the 41Ca/Ca results through a series of measurements of reference samples, and performed demonstration analyses on bone, rock and seawater samples. Our table-top method has the potential to explore the suitability of 41Ca as a tracer.The calcium isotope 41Ca is a promising candidate to complement dating methods relying on radiocarbon. Small levels of 41Ca can be measured with atom-trap trace analysis, which brings the use of 41Ca a step closer to applications.