Tagging methods are needed for both adult and juvenile life stages of Pacific lampreys Lampetra tridentata to better understand their biology and factors contributing to their decline. We developed a safe and efficient technique for tagging juvenile Pacific lampreys with passive integrated transponder (PIT) tags. We tested the short-term survival of PIT-tagged juvenile lampreys in freshwater at four temperatures (9, 12, 15, and 18°C) and their long-term growth and survival in seawater. For both experiments there was little to no tag loss, and juvenile lampreys in freshwater showed high survival at all temperatures at 7 d (95–100%) and 14 d (88–100%) posttagging. Prolonged holding (40 d) resulted in significantly lower survival (28–79%) at warmer temperatures (12–18°C). For juvenile lampreys tagged in freshwater and then transitioned to seawater, survival was 97% for tagged fish until day 94, and at the end of 6 months, survival was about 58% for both tagged and control fish. About half of the tagged and control fish that survived in seawater grew, but there was no difference in growth between the two groups. In freshwater, but not in seawater, most fish that died had an aquatic fungal infection. In both experiments, survival increased with increasing fish length at tagging. Our results indicate that tags similar in size to a 9-mm PIT tag are a feasible option for tagging metamorphosed juvenile lampreys migrating downstream and that when fungal infections are mitigated—as in seawater—long-term (at least 6 months) survival of tagged juvenile lampreys is high.