Microchip implantation is commonly performed in dogs, with only rare reported adverse events. We report the diagnosis and clinical implications of abnormal pulmonary arterial migration of identification microchips in two dogs. The first dog, an 8‐year‐old Siberian Husky, was presented for acute dyspnoea. Thoracic radiographs revealed the presence of a small, metallic foreign body in the right caudal lung lobe. Computed tomography confirmed that the foreign body was a microchip located in the right caudal pulmonary artery. Pulmonary hypertension was identified on echocardiography and was suspected to be secondary to the microchip erratic arterial location. The microchip was surgically removed through arteriotomy. The second dog was an 11‐year‐old crossbreed. The microchip was incidentally identified on computed tomography in the left pulmonary artery, whereas no clinical sign attributable to pulmonary or vascular abnormality were identified. We hypothesised that both microchips migrated via the right heart cavities after inadvertent intrajugular insertion.