"If there has been a confirmed or suspected period of loss of consciousness, the player must be removed from the field of play, and not be allowed to return," an FA document said.
It said professional players should also undergo baseline neuro-psychological testing at the start of each season and not be allowed to return to action for six days after suffering a head injury causing unconsciousness or concussion.
Head injury charities branded Tottenham Hotspur "irresponsible" last season when goalkeeper Hugo Lloris was allowed to play on despite a heavy blow to the head sustained in a challenge with Everton's Romelu Lukaku during a Premier League match.
The incident raised question marks about clubs' handling of head injuries and sparked a debate in the House of Commons about the dangers to sportsmen and women while world players' union FifPro said the Lloris incident was "unacceptable".
The new guidelines, designed to clarify the club's responsibilities, were welcomed by brain injury association Headway.
"We are pleased to see the football authorities have addressed the serious issue of concussion," said Peter McCabe, chief executive of Headway.
"The measures announced today are a significant step forward in the protection of footballers at all levels and therefore are warmly welcomed.
"The guidelines at all levels, from FIFA to the FA and Premier League, have to date been insufficient and ineffective, as demonstrated by numerous high-profile examples.
"The debacle with Spurs' Hugo Lloris, who was allowed to overrule his club doctor and return to the pitch having sustained a serious head injury in collision with Everton's Romelu Lukaku, was truly shocking.
"Since then, there have been numerous other examples of FIFA and FA guidelines being breached, including two incidents in the World Cup."
Uruguay's Alvaro Pereira and Argentina's Javier Mascherano were both allowed to continue playing during the World Cup despite clear signs of concussion while Germany's Cristoph Kramer appeared to lose consciousness in the final and was only substituted several minutes later.