Four mountain rescue teams were called to separate incidents at the summits of Corn Du and Cribyn.
One person is being treated at Swansea's Morriston Hospital for burns. The other is at Prince Charles Hospital in Merthyr Tydfil.
Some rescuers were training in the area when the incidents happened.
An RAF Sea King from Chivenor was sent to aid two casualties on Cribyn and road ambulances and police were also sent to the scene.
Brecon Mountain Rescue Team were ending their exercise due to the electric storm when they received a call-out.
Its team doctor reached the first male casualty on Corn Ddu within 35 minutes.
Spokesman Mark Jones said passing cadets who had been on the summit at the time of the strike had already started resuscitation when the rescue doctor took over.
"I've been in Brecon Mountain Rescue for 30 years and I've never known anything like this," he said.
"It is exceptionally unusual, and for multiple people to be hit in multiple strikes on different peaks - it is very, very rare."
Three other mountain rescue teams - Central Beacons, Longtown and Western Beacons - were also called out.
A Dyfed-Powys Police spokesperson said: "As a result of these incidents, two men have sadly died, one man is in a serious condition in hospital and another man is in hospital but did not sustain serious injuries.
"Officers have informed the next of kin of the deceased men."

The 55-year-old tweeted from the hospital in Tooting to thank the professionals who "saved his life".
Moore won 64 England caps between 1987 and 1995, played for the British and Irish Lions, and trained as a solicitor while pursuing his rugby career.
The former England hooker now works in the media.

The suspect was tracked down at the Underground station for Heathrow Terminals one, two and three.
Earlier, armed officers carried out a search on a Victoria line train at King's Cross St Pancras Underground station following reports of an incident at Finsbury Park.
The victim suffered cuts to his body and face and was taken to hospital.
British Transport Police said his injuries were not thought to be life-threatening.
A spokesman told the BBC armed officers attended because they had been on patrol nearby.
The Victoria line was suspended in both directions for around 15 minutes.  It has since reopened but is severely delayed, a Transport for London spokesman said.
Liam O'Hare, who was at Finsbury Park at the time of the incident, told BBC London he saw an altercation between two men on the southbound Victoria line platform.
He said: "One of the guys ran off in a different direction, and one boarded the train but was immediately helped off as he was clearly injured.
"He was bleeding, there was a puddle of blood on the train floor and people had to step over it."
He added that other passengers reported seeing one of the men holding a blade, but said he had not seen it himself.
Two men are being treated in hospital after lightning strikes in the Brecon Beacons which killed two other men on Sunday.
[NEXT_CONCEPT]
Former England rugby international Brian Moore is recovering in intensive care at St George's hospital in London after suffering a heart attack.
[NEXT_CONCEPT]
A man has been arrested on suspicion of grievous bodily harm after an assault on a 63-year-old man at Finsbury Park.