Early findings from on-going research by the Future Leaders Trust show that when school leaders become mothers their pay, training and promotion opportunities all suffer.
However, the same research has found that becoming a father tends to benefit the careers of male headteachers.
The warning comes after Future Leaders recently raised concern that there were 1,700 "missing" female headteachers in England. This is because, according to government data, while 74 per cent of teachers in the English state system are women, only 65 per cent of headteachers are women. If these figures were equal, there would be 1,700 more female heads.
The new findings come from an on-going Leadership and Parenthood Survey, which has so far been completed by 114 men and 171 women.
Initial results show that more than half believe women's pay is negatively affected by motherhood, while 60 per cent said that training opportunities were hit.
Meanwhile, more than 75 per cent said that both promotion and opportunities for additional responsibilities were negatively affected by motherhood.
The results also show that, on reaching headship, mothers are more likely than fathers to start in the bottom third of the advertised pay range, while fathers are far more likely than mothers to start headship in the highest pay band.
Notably, nearly half of the female heads responding have one or no children, while more than 80 per cent of male head respondents have two or more children.
Furthermore, the early results suggest a "fatherhood bonus", with male heads less likely to feel a negative impact on promotion and pay. They also reported being received positively by governors and parents.
Kate Chhatwal, chief programme officer at Future Leaders, said: "These findings help explain something we've seen across England's schools: women find it hard to get to the top jobs and mothers can find it even harder.
"The negative perceptions around motherhood showed up in our research through a variety of ways, from sniping colleagues, to diminished salary and promotion opportunities. One woman spoke of pay being docked when she was off because her child had chickenpox, despite having an otherwise unblemished attendance record.
"This has to change. We need more heads who consciously act as role models by being great at their job and shaping it to fit their family commitments, changing school routines to make them compatible with the rhythms of family life. We can't afford for our children to miss out on a pool of exceptional school leaders simply because leadership is seen as incompatible with being a parent."