Neymar's father has played a key role in his son's career and founded the agency NR Sports, which holds the rights to the Santos player's name and image.
According to reports in Brazilian media, Neymar Sr.'s contract runs until December, and he will stay on in the role if Santos president Marcelo Teixeira is re-elected next month.
Santos are ninth in the Brazilian Serie A standings with 47 points from 34 matches.
"We have been working daily to find solutions and alternatives to improve Santos's situation and strengthen our management," Teixeira said in a statement.
"The arrival of Neymar Sr. as the new CEO represents one more step in this process. I am confident that, with his experience and knowledge, we will be able to move forward even further and, together, build an ever-stronger club."
Former Barcelona and Paris Saint-Germain player Neymar, Brazil's all-time leading scorer with 80 goals in 130 appearances, returned to his childhood club Santos in 2025.
He was part of the Brazil squad at this year's World Cup in North America, but in late July said he no longer wanted to play for the national team, weeks after suggesting his international career had ended following their last-16 defeat by Norway.
