No, the character of Francis from Malcolm in the Middle was played by Christopher Masterson (born Christopher Kennedy Masterson on January 22, 1980 in Long Island, New York). Christopher is the brother of Danny Masterson from That 70's Show. You can look forward to seeing Masterson later this year in the film Chapman.
The character of Barney from How I Met Your Mother is played by Neil Patrick Harris (born June 15, 1973 in Albuquerque, New Mexico). Harris played the young character Doogie Howser, in the series Doogie Howser M.D. (1989).
Harris has appeared in 155 episodes of How I Met Your Mother so far, and will also be appearing in American Reunion which opens in theater on April 6, 2012.