The capital city outfit host Ulster on Friday night in the RaboDirect PRO12 and Scott has made five changes to the side that lost 14-13 to Llanelli Scarlets in Michael Bradley's last game in charge.
Gilchrist returns after making his Test debut in Saturday's 23-18 defeat to the French in Paris, while three of his Scotland team-mates - wing Tim Visser and front-row forwards Ross Ford and Geoff Cross - take their place amongst the replacements.
Scott, who only took up his interim post on Monday after concluding his duties with the Dark Blues, where he assisted Scott Johnson as special skills coach, knows his side face a tough task against their Irish opponents, who sat top of the league for four months until just one win from their last four matches saw them overtaken by Glasgow.
But Ulster's form still compares favourably to their hosts', however, who go into the match seeking their first championship success after seven successive defeats.
Despite the difference in standings, Scott says the players and management are taking confidence from a quality week preparing for his first match at the helm.
He said: "The players' reaction in training this week has been excellent. It's been a tough season but their commitment to improving and getting results for the club and its fans has been superb.
"A lot of hard work has gone in this week but, importantly, the work done has also been of a very high standard. There's a real will to do whatever it takes to get our results back on track."
Scott has made three changes to the pack for the Ulster clash, with international back row Ross Rennie returning from the shoulder injury he sustained in Scotland's autumn Test against New Zealand in November. Netani Talei replaces the injured David Denton (knee) at number eight, while lock Gilchrist is also back in the side.
Both Scott and interim assistant coach Duncan Hodge have seen enough of promising young scrum-half Sean Kennedy from his Scotland A success to hand the 21-year-old his Edinburgh debut, and Ben Atiga returns to inside centre for his 10th appearance in the competition alongside Dougie Fife.
- Sports & Recreation