A method for controlling an endodontic instrument, wherein an endodontic file (11) mounted on an assembly micromotor (8)-contra angle (9) is rotated in a first direction (working angle, ´) and successively in the opposed direction (unloading angle, ·) with an alternated movement. According to the invention, the inversion of the direction of rotation occurs with sinusoidal acceleration of the speed of rotation, from zero to the working value. System comprising a micromotor (8) and a contra angle (9) with alternated movement of an endodontic file (11) in a first direction (working angle, ´) and successively in the opposed direction (unloading angle, ·) within an alternated movement, characterized in that it, comprises a control unit (60) of said micromotor rotation, generating a control signal of the acceleration of said micromotor with the shape of a sinusoid wave causing the inversion of the direction of rotation occurs with sinusoidal acceleration of the speed of rotation, from zero to the working value.
