Emerson Valley School will fine parents of pupils who consistently arrive late.
The school will impose a £60 fixed penalty if children miss registration 10 times in a 12-week term.
The junior school, which is reported as being in special measures, says it is trying to raise standards.
If the fine is not paid within 21 days, the fine will increase to £120.
Milton Keynes Council said a borough-wide policy was in place, but the final decision on whether to issue the penalties was down to individual schools.
The fixed penalty notices are backed by law and parents who do not pay can be prosecuted.
“Our figures show that in the last academic year, two fixed penalty fines were issued in relation to persistent late attendance by pupils,” said a spokesman for the council. “In the majority of cases a warning letter has proved to be enough to stop the issue.”
A spokesman for Emerson Valley School said it was liaising with Merebrook Infant School in Furzton regarding timings of the school day.
A statement from Emerson Valley School said: “The link between good attendance and pupils achieving well at school is clear.
“During the recent OfSTED monitoring inspection it was noted that “strategies to improve attendance and punctuality have resulted in a significant increase in the proportion of pupils who come to school on time”.
“At the end of the Autumn term 2013, 353 pupils at Emerson Valley School received certificates for 100 per cent punctuality.
“This is a big improvement on previous years and has been achieved through working with our families.
“National and local authority guidance is that as a last resort, a Fixed Penalty Notice may be issued for persistent late arrival at school. At present Emerson Valley School has not issued a warning letter or Fixed Penalty Notice during the current academic year for persistent late arrival.
“Emerson Valley School has liaised with Merebrook regarding timings of the school day and has taken positive steps so parents can ensure that their pupils can be punctual for the start of both schools days.
“The playground at Emerson Valley School is open from 8.40am, when staff are on duty.
“Emerson Valley School is currently working with a number of other local school to further develop good attendance and punctuality practices, using national and local guidance.”