Therapeutic hypothermia has become standard treatment for neonatal hypoxic–ischemic encephalopathy (HIE), with brain MRI commonly performed after the child has been rewarmed. However, early imaging during hypothermia might provide information important in designing clinical trials that refine and personalize therapeutic hypothermia. We tested a protocol to ensure safety and maintenance of hypothermia during in-hospital transport and MRI. MRI during therapeutic hypothermia was performed in 13 newborns on the 2nd-3rd postnatal days. Mean one-way transport time was 20.0 ± 3.3 min. Mean rectal temperatures (°C) leaving the unit, upon arrival at the MR suite, during MRI scan and upon return to the unit were 33.5 ± 0.3°C, 33.3 ± 0.3°C, 33.1 ± 0.4°C and 33.4 ± 0.3°C, respectively. Using our protocol therapeutic hypothermia was safely and effectively continued during in-hospital transport and MRI without adverse effects.