Tiger Woods walked the course watching his son but tournament rules prevented him from serving as Charlie's caddie at Oakland Hills Country Club in suburban Detroit.
Charlie Woods birdied both par-5 holes but also made four bogeys and five double bogeys on the North Course and will play the South Course on Tuesday afternoon.
Woods was near the bottom in a field of 264 golfers who will use 36 holes of stroke play to determine 64 places in match play competition that starts on Wednesday.
The winner of Saturday's 36-hole final captures a berth in the 2025 US Open at Oakmont.
Tiger Woods won the US Junior Amateur in 1991, 1992 and 1993. The only other player to win the crown more than once was Jordan Spieth in 2009 and 2011.
The elder and younger Woods have teamed up at the PNC Championship the past four years, finishing as the runners-up in the parent-child event in 2021.