Women and men joined the event in Islamabad, the largest such rally in the country, for what is known in Pakistan as the Aurat March, using the Urdu word for women.
Dozens of men and women from the Red Mosque brigade, consisting of several local militant groups, staged a rival rally just across from the women's march venue, District Deputy Commissioner Hamza Shafqaat said.
Police official Mazhar Niazi said the officers blocked the Islamists as they tried to break through a cordon to attack the marchers.
A Reuters witness and Niazi said the Islamists threw stones, bricks, sticks and shoes at the marchers. Niazi said no one was injured.
He said a criminal case would be registered against the Islamists for violating the law and attempting to attack the women march.
There has been an uproar in conservative circles over slogans used at the past two such events, including "My body, my choice," "My body is not your battleground" and "Stop being menstrual phobic."
Following last year's event, organizers said they faced a backlash including murder and rape threats.
Ahead of this year's event, organizers say posters and murals were vandalized, including one by the Islamists from the Red Mosque.
Marches in other parts of the country were held peacefully amid tight security.
A court in the eastern city of Lahore allowed the march there to take place on condition that organizers and participants adhered to "decency and moral values."