The 16-year-old had undergone a number of trials around clubs in the UK including Manchester United, Brighton and Southampton who were all interested in taking him on.
However, the U17 international has agreed a one year contract with an option for three further years.
Karl Jakob Hein (left) joined Arsenal on the advice of his mentor Mart Poom (right)
Hein, who played for Nomme United in Tallinn, was advised by mentor Mart Poom the former Derby County and Arsenal goalkeeper who is Estonia’s goalkeeping coach.
With Hein arriving at the club, initially on a scholarship deal, it could lead to fellow goalkeeper Arthur Okonkwo leaving.
Hein, who played for Nomme United, has been capped by Estonia at U17 level
Okonkwo has been offered scholarship terms by Arsenal but has yet to commit his future to the club and has been targeted by Celtic and RB Leipzig.
Arsenal have a host of talented young goalkeepers on their books, including Joao Virginia, who part of the Portugal youth squad for the upcoming Toulon Tournament.