Zirconolite is an accessary mineral occurred in the lunar basaltic and granitic rocks and contains relatively high contents of U, Th, and Pb, which is attractive for age dating. However, very few studies have reported the crystallization ages of lunar zirconolites because of the challenge of dating lunar zirconolites due to their fine-grained size and irregular shape. In this study, we analyzed zirconolites in a granitic clast of the lunar meteorite DEW 12007 using an electron microprobe. MAN (mean atomic number) background, peak interference, and blank corrections were applied to 31 elements including U, Th, and Pb, and REEs, to obtain high-precision and high-accuracy chemical data of the zirconolites. The electron microprobe age of the zirconolites is determined to be 4332 ± 14 Ma (2σ, n = 20), which is consistent with the U–Pb age (4340.9 ± 7.5 Ma; 2σ) of zircon grains from the same clast measured by an ion microprobe. The precision and accuracy achieved in this study represents a notable advance compared to previously reported electron microprobe ages of lunar zirconolites. This suggests that electron microprobe dating may be applicable to extraterrestrial materials, especially for microscopic U-Th-Pb-containing minerals in the samples returned from the Moon and Mars.