McNerney also caught three passes for 68 yards.
Potomac School coach Rob Lee said McNerney has been impressive.
"Conor McNerney is in exceptional shape and he has worked so hard in the weight room," Lee said. "He came into the game with 550 yards. He now has seven touchdowns on the year. I think our offense is going to continue to get better. We have a lot of weapons. We try to distribute the ball to everybody and today it worked."
Saint James (2-2, 0-1) trailed 35-14 with less than a minute remaining in the third quarter.
The Saints rallied to chop the Panthers' lead all the way down to 35-33 with 6:59 to go in the fourth quarter.
Saints quarterback Jamie Peterson scored from the 1 and threw touchdown passes covering 66 yards to Dylan Zimmerman and 65 yards to Mande Magassouba in the comeback effort.
From there, Potomac School took over as McNerney scored his third touchdown on a 1-yard run through the middle with 3:59 left in the game to extend the lead to 41-33.
Forrest Ackerman added a 1-yard touchdown run for the Panthers with 46 seconds remaining to provide the final margin.
"It was a tough game," Saint James coach Chris Milmoe said. "Potomac is a great team. Conor McNerney was a well-balanced running back. He makes people miss and he breaks tackles. They had some very nice big plays. Our kids responded well. We only had 15 offensive plays in the first half, including just four in the first quarter. The kids just kept fighting until the end. They really showed their character."
Edwin Kuhn completed 18 of his 33 passes for 313 yards and added two touchdown passes for Potomac School. Mikey Duffy had 134 receiving yards and Ian McNerney made two interceptions for the Panthers.
Peterson finished with 329 passing yards, as he threw three touchdown passes and ran for another touchdown for Saint James. Kevin McCormack had 113 receiving yards on two catches, Dylan Zimmerman added 98 receiving yards on four catches and Mande Magassouba had 87 receiving yards on three catches for the Saints.
"There are still a lot of games," Milmoe said. "I feel that the outlook for the rest of the season can be good if the kids respond well. We just have to come back out and work hard."