The former Portugal attacker will depart at the end of the season to become head coach of Guinea-Bissau.
Formerly of Arsenal, Boa Morte held legend status at Craven Cottage after scoring 54 times in 250 appearances before his return as a coach.
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Boa Morte joined manager Marco Silva's staff in 2021.
The club stated: "Everyone at Fulham would like to thank Boa for his efforts since his return to the Club, and wishes him the best of luck in this next chapter when he departs following our season finale away to Luton Town."