The 59-year-old replaces Daryl McMahon, who left the club on Wednesday after more than three years in charge.
"I can't wait to get going. This is a fantastic football club and the hard work starts now," he said on the club's website.
Ebbsfleet chairman Dr Abdulla Al Humaidi added: "Gary has a proven track record in almost 30 years of management and his exceptional experience was what stood out for us when considering who to entrust with the next steps forward for this club."
McMahon left despite Saturday's 1-0 win over Barrow.
During his time in charge Ebbsfleet won promotion to the National League and last season they secure play-off place before falling just short in the semi-finals against eventual winners Tranmere Rovers.
"Naturally, this is a disappointing day for myself and the board in parting ways with someone who has been part of the very fabric of our club for the past three years," the owner said.
"However, we believe it is the right decision for the club at this point in our development on and off the field. We wish Daryl all the very best in his future career and reiterate our thanks for all he has accomplished in getting the club to its current position.”