It found a Sebastopol father guilty of shaking his seven-week-old baby that left a baby boy with severe and lasting brain injuries.

The jury returned to the County Court Tuesday morning after retiring at noon on Monday and handed down a guilty verdict on Sebastopol man Jesse Thomas Harvey's charge of recklessly endangering and causing injury to the infant.

A further charge of negligently endangering the child was dismissed.

Thomas Harvey had pleaded not guilty to the charges after his son Casey was admitted to the Ballarat Base Hospital with head injuries on April 19, 2017.

Judge Gavan Meredith has set the sentencing down for a later date allowing the defence six weeks to have Harvey undergo a psychological assessment.

Earlier in the trial Harvey's defence barrister told a Ballarat jury there was ample time in the early hours of the morning for a man to shake his brother's baby, causing severe brain damage.

Tim Sullivan told the County Court jury during closing addresses on Friday his client, Jesse Thomas Harvey, was telling police the truth when he said he did not shake his seven-week-old baby at his Sebastopol home on April 19, 2017.

But police allege the 21-year-old seriously injured the baby sometime between 2.30am and 12.46pm because he told detectives he was with the baby the whole time.

Crown prosecutor Gary Hevey said Harvey did not tell the truth during the record of interview and he "shook his baby so hard ... that this child's life is effectively over".

Casey was diagnosed with a number of head injuries, including subdural haematomas, retinal hemorrhages, swelling on the brain, diffuse axonal injury and torn posterior neck ligaments.

He is now severely disabled, requires high-level care and has a poor prognosis.

Mr Hevey said during the record of interview, Harvey did not suggest his brother or mother caused the injuries, but said his mother was a loving, caring grandmother, while his brother was an excellent uncle.

He told the jury Harvey "freaked out" when he woke about 10.30am, well past Casey's usual feeding time, to find him "staring up into space" with his hands in the air.

But Mr Hevey said it took him until 12.46pm to take Casey to hospital in a taxi.

He said Harvey went to a shop to buy credit to phone his sister and he entered the taxi with a take-away milkshake.

"This is not consistent with someone freaking out at 10.30am," Mr Hevey said.

The prosecutor drew the jury's attention to forensic paediatrician Dr Jo Tully's evidence where she confirmed Casey's injuries were caused by shaking, not by playing ring-a-ring-a-rosy.

Mr Hevey said Dr Tully believed the baby's injuries occurred closer to the taxi trip to hospital than earlier in the morning.

She had told the jury Casey's injuries were seen in children involved in car accidents or a 10-metre fall, not normal mechanisms of play, including ring-a-ring-a-rosy.

Harvey's counsel said there was a reasonable view of the facts consistent with the innocence of the accused.

He has pleaded not guilty to recklessly and negligently causing serious injury.

The trial will continue on Monday when Judge Gavan Meredith with give his legal direction to the jury.