The petrochronological records of eclogites in the Scandinavian Caledonides are investigated using EPMA and LA-ICPMS of zircon and apatite for U–Pb geochronology, combined with major and trace element characteristics. Metamorphic zircon from two eclogites from the Lofoten-Vesterålen Complex (Lofoten Archipelago region) collectively yielded a Concordia age 427.8 ± 5.7 Ma and an upper intercept U–Pb age 425 ± 30 Ma. Apatites from the same eclogites provided U–Pb lower intercepts at 322 ± 28 Ma and 354 ± 33 Ma, with the latter also yielding a younger age of 227 ± 24 Ma. Two eclogites from the Lower Seve Nappe (Northern Jämtland) demonstrate different zircon and apatite age records. Metamorphic zircon provided Concordia ages of 467.2 ± 5.9 Ma and 444.5 ± 5.5 Ma, which resolve the age of prograde metamorphism and zircon growth during retrogression, respectively. The lower intercept U–Pb ages of apatites from the same eclogites are 436 ± 18 and 415 ± 25 Ma, respectively. In combination with their geochemical characteristics, they suggest two separate stages of exhumation of eclogite bodies in the Lower Seve Nappe. Zircons from an eclogite from the Blåhø Nappe (Nordøyane Archipelago) yielded a continuum of concordant U–Pb dates from ca. 435 to 395 Ma, which suggests several cycles of HT metamorphism within short intervals. Distinctive trace element characteristics of apatites from the Blåhø Nappe eclogite suggest formation coeval with zircon and garnet during HT metamorphism, but Pb diffusion behaved as an open system until cooling during exhumation of the nappe at 390 ± 12 Ma (lower intercept U–Pb age of apatite). To summarize, this study presents the high potential of coupled zircon and apatite petrochronology of eclogites in resolving their metamorphic evolution, particularly with respect to using trace element characteristics of apatites to constrain the records of their growth, alterations and the meaning of their U–Pb age record.