A Brisbane builder accused of sexually assaulting his young son took almost four years to clear his name through the courts and secure access to the child, a period that took more than half the child's life.

In a case that highlights the slow pace of the Family Court system, the now 30-year-old man applied to the Federal Circuit Court for access to his two-year-old son in April, 2015.

After being transferred to the Family Court a year later, the case was finally resolved a week before Christmas by three judges. They took five months to rule the man had not assaulted the boy and should have primary custody.

A Brisbane mother who accused her ex-partner of sex abuse lost custody. The case took almost four years to resolve. supplied

Now five-and-a-half, the boy wasn't allowed to be alone with his father for two years.

The man, who cannot be legally identified, said he was grateful the court system had investigated the claims against him thoroughly and he didn't feel there was any bias against fathers, which is a complaint among some anti-Family Court activists.