Varley is no stranger to this situation. He was drafted into the Ireland squad that toured New Zealand and Australia in June of last year, coming in as cover for the sidelined Flannery.
Flannery has been beset by injury problems in recent seasons which have severely limited his game-time with both Munster and Ireland.
He won his 41st cap as a second half replacement against the USA, having had four outings during the World Cup warm-up schedule.
His latest injury blow opens the way for fellow Munster hooker Varley to play on the biggest stage of all and add to his two previous caps against Australia and Argentina.
"There were a couple of emotions running through my head when I got the call from Declan (Kidney) inviting me to join up with the squad," said Varley, a solid lineout operator who scrummages and carries with considerable power.
"The first was obviously overriding elation at getting the opportunity to take part in the tournament. You always dream of representing your country at the highest possible level and the World Cup is the pinnacle of the sport.
"After the initial excitement, my thoughts turned to Jerry's position. I know he'll be gutted at having to return home early after what has been a hard journey for him to get his fitness back, but I am sure he will be looking to get back playing as soon as possible.
"The best possible compliment I can pay him is to make sure that I train hard down there (in New Zealand) and do whatever I can to help the squad be as successful as possible."
The 28-year-old, who won a senior treble with Garryowen in the 2006/07 season, made the international breakthrough last year after his best season yet with Munster.
He was a member of the Ireland training squad during the summer, so his move from playing for his province in the RaboDirect PRO12 to rejoining the national set-up should be a smooth one.
"I've been able to maintain my fitness levels with Munster and kept my game-time ticking over with them, so I feel fresh and ready to do whatever is asked of me," he admitted.
"I was part of the extended Ireland squad for the pre-season, so a lot of the technical stuff and calls are still fresh enough for me to be able to hit the ground running.
"We have a massive game this weekend against Australia and I will just about make it to Auckland in time to see it."
Follow the Ireland team in New Zealand on www.twitter.com/irfurugby.