Argentina coach César Menotti included Hernández in the 1982 FIFA World Cup squad as his third choice for creative midfielder, behind Diego Maradona and José Daniel Valencia.

Hernández has had a heretofar unsuccessful coaching career, including Estudiantes, Racing Club, and other teams in South America, mostly in Ecuador.

In February 2007, Hernández was hired as coach of Club Atlético Banfield from the Argentine premiership, but he was fired March 16, 2007 after a home defeat to Estudiantes.

Hernández is also a respected football commentator with Argentine sports network Torneos y Competencias where he does in-depth tactical analysis, usually assisted with video clips and props.

His niece and Juan Martín's older sister María de la Paz Hernández is an Argentine international in field hockey.