He is now claiming damages and demanding the school returns the phone, arguing that it has infringed on property rights.
The school, one of Singapore’s most prestigious, declined to comment when contacted.
The BBC has also sought comment from the father.
The use of mobile phones in schools has been a controversial issue in many places. In 2006, a group of parents in New York sued education authorities over a similar ban, but eventually lost. The ban was lifted in 2015.
‘May send the wrong signal’
In a January circular to parents, the school reiterated its ban on mobile phones saying they “pose a distraction from learning” and that students should keep their mobiles and other electronic devices in their lockers during school hours.
The school said that it would confiscate offenders’ phones for three months.
The man had lent his iPhone to his son, and it was confiscated on 21 March after the boy was caught using it during school hours, according to court documents.
The boy was told the phone would be returned after the three month confiscation period.
The father has since filed a lawsuit claiming an unknown amount of damages, as well as a legal injunction demanding the phone be returned immediately while the case proceeds.
The lawsuit is pending, but a judge has rejected the injunction, saying the confiscation was “justifiable” as the principal was enforcing the school’s rules.
He added that returning the phone prematurely may result in the school being “faced with demands from parents or guardians for the return of confiscated phones”.
“This may also send a wrong signal to the students that they can use their mobile phones during school hours with impunity,” the judge said.
Update 8 June 2017: Some details in this report have been changed to ensure those involved are not identified.