Vanmarcke, 32, has signed a three-year contract and will lead the line for the team in the Spring Classics, with current leader Nils Politt moving to Bora-Hansgrohe.
He follows seven-time Grand Tour winner Chris Froome, as well as Michael Woods, Daryl Impey, Carl Fredrik Hagen, Patrick Bevin and Alessandro De Marchi in a raft of arrivals at Israel Start-Up Nation for 2021.
"They’ve built a strong group of riders for the next years – a combination of great riders already with the team and some big names who are joining them. I’m happy to be part of that group," Vanmarcke said.
"I see how the team is growing. In only a few years it went from being a small team to a WorldTour team. Now that is has reached that level, it aims higher. And I do too."
Vanmarcke leaves EF Pro Cycling after four years, and six in total. He began his WorldTour career with Jonathan Vaughters squad in 2011 when it was known as Garmin-Cervélo and subsequently spent four years at the team now known as Jumbo-Visma before returning in 2017.
Vanmarcke has been a perennial contender in the major cobbled Classics but a lack of a fast sprint finish means he has yet to land the big victory that has always seemed within his grasp. He won Omloop Het Nieuwsblad in 2012 but has since then been consigned to the podium places or the top-five.
"He has a lot of experience," Israel Start-Up Nation manager Kjell Carlström said of Vanmarcke.
"He has proven that he is a great Classics rider but can also support a leader in a Grand Tour. And he also does well in time trials, so it is a perfect package."
Vanmarcke will link up with sports director Eric Van Lancker, who he rode for at Garmin back in 2012, and he'll also find the Belgian national coach Rik Verbrugghe, who's joining Israel Start-Up Nation as a director next year. It's unclear if Ken Vanmarcke, Sep's brother, will remain as a director at EF Pro Cycling or if he'll transfer across too.
"He is a strong rider for the Flemish Classics and he will be our leader," said Van Lancker.
"He is a rider who can be top and he will certainly get all our help to succeed. I am looking forward to working with him again."
Vanmarcke is Israel Start-Up Nation's ninth signing for 2021, following Froome, Woods, Impey, Bevin, De Marchi, Hagen, and neo-pros Taj Jones and Sebastian Berwick.
EF Pro Cycling have now lost both Vanmarcke and Woods to Israel, although Alberto Bettiol has extended his contract and is set for sole leadership in the Classics.
The American team also say goodbye to Daniel Martínez, who's off to Ineos Grenadiers and Tanel Kangert (Mitchelton-Scott). They have so far announced the signing of Japanese rider Hideto Nakane from Nippo Delko One Provence.
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