Cryptoy allows users to learn about the history of encryption and create their own encoded messages. These can be shared on social media and deciphered by friends.
GCHQ hopes the app, which will be available to download from the Google Play store, will be used in schools to teach kids about coding.
The launch of the app comes on the third anniversary of the U.K.'s Cyber Security Strategy, aimed at protecting Britain from cyberattacks in an increasingly hostile digital world.
Security researchers have discovered a number of major state-backed cyber attacks this year. In one unveiled by U.S. security company FireEye, Russian hackers were carrying out a long-running cyber espionage campaign targeting key institutions like NATO.
"Building maths and cyber skills in the younger generation is essential for maintaining the cyber security of the UK and growing a vibrant digital economy," Robert Hannigan, director of GCHQ said in a press release.
The app was designed by interns at GCHQ and runs through four key encryption techniques: Shift, Substitution, Vigenère and Enigma.
GCHQ has been the focus of controversy over the way it monitors data and electronic communications following revelations by former National Security Agency contractor Edward Snowden. But the spy agency said that users should have no privacy concerns over the app.
"Cryptoy is purely an educational app, and doesn't require any permissions to access personal data or enhancements to be made to your device when installing," GCHQ said on its website.
The launch of the app comes as the U.K. government gets set to announce grants for colleges and universities in Birmingham, Liverpool, London and Newcastle to improve cybersecurity education. "Cyber camps" to help computing graduates gain work experience in the cyber security industry will also be unveiled on Friday.