Prop Adam Macklin comes into the matchday 22 in place of Jack O'Connell.
In addition, out-half Andrew Burke, who started the first game of the Championship against France, has returned from injury and been added to the bench in place of Gary Foley.
Coach Clarke said: "The win against England was a reflection of the strength of the squad's character and resolve.
"However, there were particular aspects of our game we were not content with and these have received special attention this week.
"Scotland has shown they are a team to be reckoned with and respected, particularly at home.
"We are aware of the competitive challenge ahead and the levels of performance required. Our aim is clear - to keep progressing and improving as individuals and ultimately as a team."
IRELAND UNDER-20 TEAM & REPLACEMENTS (v Scotland Under-20s, 2009 RBS U-20 6 Nations Championship, McDiarmid Park, Perth, Friday, March 13, kick-off 7.30pm):
15 - David Kearney (Lansdowne/Leinster)
14 - Ronan O'Mahony (Garryowen/Munster)
13 - Ian McKinley (UCD/Leinster)
12 - Eamonn Sheridan (Lansdowne/Leinster)
11 - Michael Keating (Clontarf/Leinster)
10 - Ian Madigan (Blackrock College/Leinster)
9 - Matthew Healy (Lansdowne/Leinster)
1 - Paddy McAllister (Ballynahinch/Ulster)
3 - Jack McGrath (St. Mary's College/Leinster)
4 - Ciaran Ruddock (Neath/Exiles)
5 - James Sandford (Queens University/Ulster)
6 - Rhys Ruddock (Millfield School/Exiles)
7 - Dominic Ryan (Lansdowne/Leinster)
8 - Peter O'Mahony (Cork Constitution/Munster) (capt)
16 - David McGregor (Ballynahinch/Ulster)
17 - Adam Macklin (Belfast Harlequins/Ulster)
18 - Mark Flanagan (UCD/Leinster)
19 - Michael Noone (Seapoint/Leinster)
20 - Conor Murray (Garryowen/Munster)
21 - Andrew Burke (Garryowen/Munster)
22 - Shane Gahan (Lansdowne/Leinster)