Thomson is replacing Tom Nash, who has joined OMD as its EMEA performance strategy director.
Based in London, Thomson will report directly to 360i Europe's managing director, Rikke Wichmann-Bruun.
Thomson has more than 12 years' experience in media and at Carat was responsible for accounts including Diageo, Premier Foods and Arla.
"John is a great addition as he brings heavyweight experience and a strong track record of results-driven work. This hire is part of our journey to becoming an ever stronger full service digital company, after a strong 2017," James Townsend, CEO of 360i Europe, said.
Carat, which is in the process of finalising a replacement for Thomson, thanked him for his work.
"Though we are sorry to see him leave us, his promotion takes him to a new role within the group at 360i - a move that underlines our aim to recognise talent and promote from within whenever we can, so he is not going far," Dan Hagen, chief strategy officer at Carat UK, said.