Ben Marshall gave Northampton the interval lead against the run of play but goals from Ahmed Deen, veteran striker Paul Furlong and substitute John O'Flynn turned it around for Barnet.
"It's nice to be up there but it's after 46 games that counts, not after only six," said Hendon. "Conceding a goal is the only thing I've got to moan about. Our first-half performance wasn't that bad but it was disappointing to concede the way we did.
"But we played very well in the second half and the substitutes made an instant impact for us. We knew Northampton weren't that quick and we managed to make our pace count and move the ball well.
"Northampton threw everything at us late on. Jake Cole pulled off one great save but apart from that we dealt with everything. We've had a lot of games lately and we need a break but it will be back to work on Monday."