Ulster on the other hand had a better rate of return in Munster's 22 after securing a try and a penalty try in the final minutes of the first half giving the Northern side a 14-9 lead going in at the break.
Munster academy centre JJ Hanrahan opened the scoring after 21 minutes converting his second penalty attempt and kicked another three points five minutes later giving his side a 6 nil lead.
Ulster were quick to respond and threatened the Munster line when number 7 Dominic Gallagher made a break off centre Luke Marshall's pop to run straight through the Munster defence, only to offload the ball forward just before the try line to sighs of relief from Munster.
Ulster were awarded a penalty after Munster hooker Kevin O'Byrne was penalised for a high tackle but number 10 Paddy Jackson failed to convert.
The Munster defence was finally stretched after 36 minutes when Steven Irvine found plenty of space in the far left hand corner to make it over the line unopposed and Jackson converted giving his side the lead for the first time.
Hanrahan added a third penalty before Munster were reduced to 14 men when number four Tom Goggin was penalised for a dangerous tackle.
The resulting play went Ulster's way as they dominated the scrums and were awarded a penalty try for continuous infringements. Jackson slotted an easy convert and Ulster went in with a five point lead at half-time.
On the return Munster closed the gap after two minutes with a fourth JJ Hanrahan penalty and Munster regained the lead when the centre struck his fifth penalty after 54 minutes when Ulster were caught offside.
This was to be Munster's final score of the evening as set-piece errors cost the home side dearly and Paddy Jackson kicked a further two out of three penalty chances, giving Ulster a 20-15 victory in Cork.
Despite not making it over the try line promising from a Munster point of view tonight were backs Hanrahan, Hircock and Kuntz who linked well together and Johnny Holland was solid at fullback.
Next up for the U20s is Connacht in the Mardyke on Friday 10th September, ko 7pm.
Munster U20s: Johnny Holland, Lucas Kuntz, Corey Hircock, JJ Hanrahan, Cathal Quinn, Garreth Quinn-McDonagh, Ronan Barry (Eoin O'Shaughnessy 57), Niall Scannell (John Randles 41), Kevin O'Byrne (James Rael 64), Paul Mullen, Tom Goggin, Shane Buckley (Capt.), Cathal O'Flaherty, Simon Hanbidge, Luke Cahill.
Replacements: James Rael, John Randles, David O'Mahony, Robert O'Herlihy, Eoin O'Shaughnessy, Daniel Horgan, Jack Costigan. Yellow Card: Tom Goggin (1st half 40")
Ulster U20s: Charlie Simpson, Chris Colvin, Stewart McIlwaine, Luke Marshall (Capt.), Michael McAuley, Paddy Jackson, Conor Spence, Andy Warwick (Conor Carey 49), Jonny Murphy, Kyle McCall, David Whann, Ian Henderson , Stephen Irvine (Paddy Marks 55), Dominic Gallagher, David McGuigan (Calum Threlfor 55).
Replacements: Darryl Maxwell, Conor Carey, Adam Best, Paddy Marks, Calum Thelfor, Blane McIlroy, Adam Bratton Yellow Card: Ian Henderson (2nd half 39")