He leaves for a new role at UK investment bank Close Brothers, walking away from his Â£972,000 salary.
Mr Howell has acquired a total of 229,188 shares worth $7.6 million and has options to buy more.
The news may come as a surprise, as Mr Howells had only had his job allocated last week following the $3.1 billion merger with Borsa Italiana.
Chairman of the LSE, Chris Gibson-Smith, and chief executive, Clara Furse, were the only other bosses to have their positions confirmed.
Ms Furse said: "Jonathan has played a central role in the exchange's transition from mutual organisation to highly successful public company.
"Having worked with him for over six years, I will miss his sound financial, commercial and strategic judgment."
Mr Howell will become the new finance director at Close Brothers in February as part of his desire for "a new challenge".