The account is believed to be subject to obligatory biennial reviews. The review process started last December and a shortlist was announced earlier this year.
Saatchi & Saatchi has held the account for the past 28 years and had retained the account in the last review in 2008.
Y&R Singapore will now oversee the defence force's brand and recruitment briefs. The WPP agency's chief client officer, Anthony Koo, and creative director Mark Fong led the pitch.
On the account win, Tanuj Philip, group CEO for Y&R Singapore, said: "This prestigious win is a loud and clear validation that Y&R Singapore's ‘Resist the usual' philosophy has been gaining traction with current and new clients."
He added that the agency would deploy the full extent of its strategic and creative offerings, including activation and digital, to "make a great brand even greater."
Marcus Rebeschini, chief creative officer Asia for Y&R, who was closely involved in the pitch, added: "For more than 25 years, agencies in Singapore have been trying to win this account because of the client's high regard for great award winning creativity. It says a lot to us that the Republic of Singapore Navy believes they have found the right new creative partnership with Y&R Singapore."