McNeilly spent five years working with the Shots Academy before taking temporary charge of the first team when Mark Molesley in October.
He breathed new life into a struggling side - winning five out of his eight games at the helm - keeping four clean sheets.
Now he takes full-time charge for the remainder of the season with a view to extend beyond then.
"The board are delighted to be able to announce Ross as permanent First-Team Manager of Aldershot Town," chairman Shahid Azeem said.
"The performances and winning record during his Interim spell stood out amongst the high-quality pool of candidates that applied. He’s come through the Academy, knows the football club and the players want to play under him."
"The Board are very excited to have Ross in charge until the end of the season where we will sit down and discuss plans for the future beyond this year. Football is always talked about as a results-based industry and Ross has produced those results and certainly deserves a ‘shot’"
McNeilly's first game in permanent charge is against Solihull Moors on Saturday.