Head Coach Graeme Eastwood's side recovered from last week's defeat away to Leinster by recording a bonus point victory against the current Champions.
The game was hosted by Co Donegal side Inishowen RFC, as they opened their new changing rooms at the club, with Ulster Branch President Philip Gregg in attendance to help unveil the new facilities.
David Maxwell nudged Ulster into an early lead with a penalty, before right winger Conor Phillips finished off a good move in the corner to make it 8-0.
The visitors got back into the game when Ciaran Vaughan touched down and Shane Airey kicked the extras to make it 8-7.
Loosehead prop Kieran Donaghy then drove over for the province's second try to extend the advantage.
The home side increased the pressure before outside centre Paul Armstrong ran in for his first try of the game, which was converted by his Clogher Valley clubmate Maxwell.
Airey kicked a penalty in reply for Munster on the stroke of half time to make it 20-10 to Eastwood's side.
Early in the second half, Player of the Match Armstrong again cut through the Munster defence for his second try, and Maxwell slotted the kick to make it 27-10 and register the last points of the day.
The rain picked up into the second half, and Ulster worked hard in defence to preserve their lead and make sure they recorded a vital victory.
Ulster Juniors v Munster Juniors, Inishowen RFC
1 Kieran Donaghy - Lurgan RFC
2 Matthew Coulter (C) - Ballyclare RFC
3 Neil Henderson - Clogher Valley RFC
4 Toby Mannus - Cooke RFC
5 Callum Foreman\ - Cooke RFC*
6 David Stinson - Clogher Valley RFC
7 Ben Riley - Limavady RFC
8 Stephen Corr - City of Derry RFC
9 Gerard Treanor - Monaghan RFC
10 David Maxwell - Clogher Valley RFC
11 Ewan Haire - Clogher Valley RFC
12 Nathan Burns - CIYMS RFC
13 Paul Armstrong - Clogher Valley RFC
14 Connor Phillips - Cooke RFC
15 Adam McDonald - Dromore RFC
Replacements
16 Malcolm Allister - Monaghan RFC
17 Angus Cunningham - Lurgan RFC
18 Ian Moxen\ - Cooke RFC*
19 Will Scott\ - Ballymoney RFC*
20 Reuben McCreery - Lurgan RFC
21 Davey Graham - City of Derry RFC
22 Charlie Williamson - Lurgan RFC
23 Stuart Wightman - Lisburn RFC
Match Day Injury Cover
24 Adam Barron - Ballyclare RFC
\*Denotes New Cap
Coaching Team
Head Coach - Graeme Eastwood
Assistant Coach - Damien Campbell
Team Manger - Jeremy Ogle
Physio - Scott Hughes