Alobaidi, currently managing director of Emirates Holidays, takes up his new position in September.
His appointment follows a restructuring of the company and a technology upgrade last year.
In a statement, Newmarket said: “The board believe they have found just the right person, with a very impressive track record in travel, to take the company on the next stage of its exciting journey.
“Under his leadership, over the past four years, Emirates Holidays has enjoyed an unprecedented period of growth.”
Prior to his current position at dnata, Alobaidi held senior management roles within Tui and First Choice.
Newmarket Holidays is known for its escorted touring and cruise holidays and employs 145 staff at its Wallington headquarters.