Gilligan's early goal settled the game at Broadhall Way against a Stevenage side who were reduced to ten men just after half-time when Darius Charles was sent off.
The League Two table now makes much happier reading for Ian Sampson whose side lie in mid-table.
"The players that came in did well and I think that shows we have got quite a strong squad," Sampson told the official club website afterwards.
"We've a lot of games coming up over the next few weeks and the squad will be tested...but I think we have got enough to get us through."