Clare joined the Gills on loan from Sheffield Wednesday on Thursday.
Gillingham's Priestfield Stadium
The Gills were trailing by two goals when Clare entered the fray, but Josh Parker halved the deficit before Billy Bingham came close to equalising for the home side.
Sean Clare (centre) in action for Accrington last season
The result saw Ady Pennock's side drop to 22nd in League One, and extended their winless run to eight matches since Good Friday.
Clare, who arrived at Sheffield Wednesday via the Nike Academy in early 2016, took to Twitter afterwards, expressing mixed emotions.
He posted: "Gutted about the result but happy to have made my @TheGillsFC debut. Unfortunate not to get a result be we will bounce back !! #Gills"
And based on the following responses, it would appear the 20-year-old made a positive impression at Priestfield.
From Today's Performance He Would Be A good Player To Sign If He Can Keep It Up— ShaunWooding (@Shaun_Wooding) 2 September 2017
Well done mate, made a difference when you came on, things are only gonna get better #UTG— GFC (@GFC_Banter) 2 September 2017
When you came on you made a difference keep it up #onwardsandupwards UTG— Jim Hawkins (@jhawks200) 2 September 2017
You looked bright when you come on lad keep on it and you'll be starting soon— Dan Harvey (@danharvey1) 2 September 2017
Two of Clare's Sheffield Wednesday teammates, Jack Stobbs and Jordan Thorniley, were also in action for Port Vale and Accrington Stanley respectively on Saturday.
Defender Thorniley played the full 90 minutes as Accrington beat Morecambe 2-1 to move up to third in League Two.