It was later revealed to have filed a flight plan to the British Virgin Islands' main airport. Branson's private island of Necker is part of the Carribean archipelago.
Her husband wasn't seen boarding the flight but Tom Nolan, the airport's executive director, later confirmed that the former president also departed Monday morning but it's not clear whether the couple left together.
The private jet, a Falcon 900EX is a French made, long range, ultra luxury corporate jet, called Galactic Girl.
The tail sports a blown up decal of millionaire Branson's iris on the tail fin, and a Virgin logo on the front of the fuselage.
The jet has a maximum cruising altitude of 36,000 feet, speed of mach 0.87. it is customized for each owner and can have office space or beds installed.
It is unclear if Branson was on board. The Virgin boss posted an Instagram video 10 hours before the plane took off which appeared to have been filmed in Necker, his private Carribean island.
The weather on Necker is significantly better than conditions in Palm Springs, which is affected by a winter storm warning.
Necker on the other hand had some rain on Monday but is predicted to be dry, sunny, and around 80f for the rest of the week.
Branson posted an instagram picture on Saturday of him with the former president during his time in office saying: "Thank you Obama."
Earlier Monday morning Obama visited the Thunderbird Country Club gym, where the former president has exercised every morning since arriving in Palm Springs.
The Obamas visited the area after attending the inauguration of Donald Trump in Washington, DC on Friday.
On Saturday he spent about five hours at Porcupine Creek golf course, the ultra-exclusive course owned by Oracle founder Larry Ellison.
Obama looked relaxed as he and a handful of secret service agents, negotiated the stunning 18-hole private course in several golf carts.
Obama was seen chatting and laughing with his golfing companions on the first day of his vacation and at one point fist bumped another golfer after watching a decent shot.
The world class private course in Rancho Mirage is one of the desert's best-kept golfing secrets and rests against a mountain backdrop with a stunning rugged landscape.
The course is by-invitation-only and Golf Digest once ranked as one of the top 20 golf courses in California.
Obama played at Porcupine Creek in February this year and back in 2014 he was spotted there during another visit to the desert to meet with King Abdullah II of Jordan.
The course is part of a huge $75million 249 acre estate owned by Ellison.
The estate named Porcupine Creek Ranch boasts a huge 18,400 sq ft main residence, eight guest houses, a pool, spa, gym and an amphitheater.
The property has played host to many benefits and charity events.
The perimeter of the estate has a privacy row of trees that blocks the prying eyes of the outside world.
It had been a dreary, wet and windswept weekend from the moment the Obamas arrived in Palm Springs.
On Friday low clouds covered the valley, temperatures dropped to a chilly 50 degrees Fahrenheit and rain flooded the streets of the city - not an ideal start to their vacation.
The weather was so bad the government plane carrying the family was diverted to March Air Force Base, some 44 miles away.
Fortunately, there was a break in conditions on Saturday and the sun came out allowing the former president to enjoy a round of golf.
On Sunday, other than a visit to the gym at Thunderbird Country Club, the Obamas avoided the rain and stayed at home, with sports fan Barack likely watching the NFL playoff games between Atlanta Falcons and Green Bay Packers followed by New England Patriots vs Pittsburgh Steelers.
