The Spurs chief became engaged in a lengthy and heated exchange with referee Mike Dean following the full-time whistle at Turf Moor on Saturday. Pochettino had watched his men slip to a 2-1 defeat - a big blow for their Premier League title aspirations.
A statement from the FA read: "Mauricio Pochettino has been charged with two breaches of FA Rule E3 following the game against Burnley on Saturday.
"It is alleged the Tottenham manager's language and/or behaviour at the end of the fixture - both on the pitch and in or around the tunnel area - amounted to improper conduct.
"He has until 6pm on February 28, 2019 to respond to the charge."
Dean has now been redirected from fourth official duties in Tottenham's game at Chelsea on Wednesday to avoid any potential for further conflict with Pochettino.
He will now be on the touchline at Manchester City v West Ham instead of Stamford Bridge, with Kevin Friend taking his place.
As the Spurs boss walked across the pitch post-match on Saturday, he spoke animatedly with Dean, who remained calm. Pochettino's Spanish assistant Jesus Perez jabbed his finger towards the face of Dean, while the Argentinian was eventually led away by Burnley defender Phil Bardsley.
Pochettino did not reveal what was said or the reason for the strength of his feelings, with the only really contentious decision appearing to be the award of a corner that led to Chris Wood's opening goal.
The outburst was out of character for Pochettino, who said before the charge was announced he would not contest any disciplinary action, admitting he may have "crossed the line".