Sarah Greenhalgh scored the only goal of the game at Oakwell with a header soon after the Clarets were awarded a free kick for a foul on Lizzy Hamer.
Some excellent goalkeeping by Lauren Bracewell helped cement the narrow victory.
The Clarets, who were promoted at the start of the season, have gone from strength to strength in the National League but their top standing hangs in the balance with chasing teams having games in hand.
Barnsley set the pace of the game with sharp passing which helped their strikers open up shooting opportunities.
Bracewell acrobatically tipped over an early shot from Drew Greene and soon covered a second that whistled an inch above the bar. Sammy Fleck’s hard work in the Clarets defence helped keep further threats at bay.
The Clarets kept the pressure and notably Leah Embley and Hamer tormented the home side’s defence with balls across goal that were marginally out of reach of incoming strikers.
The breakthrough goal came on 34 minutes when Embley made a piercing run on the right wing and passed to Hamer who was fouled on the edge of the area.
Embley floated over the free-kick that dropped beyond the far post where Vikki Eastwood picked out Greenhalgh in the box who smartly headed home.
Barnsley went close before the break with the final shot of the half forcing the superb Bracewell into a diving save that she smothered at the second attempt.
The Clarets came out in the second period in a determined manner and pressured the home side with a series of corners and a shot from Greenhalgh that was saved at the near post.
It took some time before the home side worked their way back into the game, though the Clarets continued to create the better chances.
Hamer fed through to Lynette Craig who cleverly spun to lose her marker and but she failed to beat Skye Kirkham at her near post.
Bracewell preserved the away side’s advantage in the latter stages, racing off her line to block from an opposition striker on the edge of the box.
Burnley had to dig in to see out the game in the last quarter and record a fourth league win of the campaign.
After usurping Chorley Ladies at the summit, coach Matt Bee said: “It’s another important three points. We know where we need to be better and we have a belief in our structure and quality.
“At this stage of a season it is nothing more than three points.
“There are lots of challenges ahead for this team and we need to be ready for them.”
Burnley FC Women compete in the third qualifying round of the SSE Women’s FA Cup on Sunday at Brighouse Town LFC. Kick-off is at 2pm.