The man who killed Caboolture toddler Mason Jet Lee has been sentenced to nine years in prison, after the 21-month-old died a "slow and painful death" in 2016, the Queensland Supreme Court has heard.

William Andrew O'Sullivan pleaded guilty to four charges before the Queensland Supreme Court in Brisbane last week, including manslaughter and cruelty to a child under 16 years old — but due to legal reasons it was unable to be reported until now.

William Andrew O'Sullivan pleaded guilty to manslaughter over the death of Mason Jet Lee. ( ABC News )

During the 37-year-old's sentence hearing, O'Sullivan's lawyer Ruth O'Gorman said he admitted for the first time that he was responsible for inflicting the blow or blows which eventually led to the death of Mason between two to five days later in June 2016.

O'Sullivan, who was the child's stepfather and primary carer at the time of his death, ignored obvious signs Mason was in pain and failed to seek urgent medical care.

The court heard Mason endured serious neglect, including in the months prior where he was left untreated for a fractured leg and other serious injuries.

In sentencing, Chief Justice Catherine Holmes said although Mason's condition would have been "wretched and painful", O'Sullivan did nothing to help him.

"He was a defenceless toddler and you seemed to have taken out your anger and frustration against him by the assault that caused the fatal injuries," Justice Holmes said.

"He was not treated with any gentleness or kindness. Worse, you did nothing to get help for him despite what would have been his evident distress."

Toddler had traces of methamphetamine in his blood

The court heard an autopsy identified widespread bruising to Mason's forehead, chest and abdomen, a broken tailbone, and traces of methamphetamine in his blood.

When paramedics were called to O'Sullivan's home in the early hours of June 11, 2016, it appeared Mason had already been dead for some time.

Mason was living with O'Sullivan at the time, while his mother lived in a separate home about one kilometre away.

Prosecutor Vicki Loury said the symptoms the toddler suffered days before dying — including vomiting, dehydration, abdominal pain and fevers — "would have been obvious to any reasonable person that he was very sick and needed urgent medical attention".

"He must've known how very, very unwell Mason was," she said.

An autopsy identified widespread bruising and traces of methamphetamine in Mason's blood. ( Facebook: Emmy Louise )

"He was the primary carer … he watched this small child in increasing levels of pain for days and did absolutely nothing to help him, which demonstrates a callous disregard for his life."

Mason eventually died from sepsis caused when his bowel was perforated by some kind of blunt force, causing faecal matter to escape into his intestine and bloodstream.

It is still not clear what O'Sullivan did to cause the injury, but Ms Loury said it was a moderate to severe blow.

"And in that context, with the age of the victim, the nature and extent of the violence was of a high degree," Ms Loury said.

The court heard in January and February 2016 O'Sullivan had failed to seek adequate medical attention for Mason's fractured shin and severe perianal injures.

The boy suffered skin loss in the perianal region similar to "that of a burn", either caused by a poor diet, lack of regular nappy changes or from a hose used by O'Sullivan to clean him.

Mason spent more than three weeks in hospital as a result, and while O'Sullivan was not the primary carer at that time, he was still partly responsible for the neglect.

O'Sullivan was addicted to meth, a self-described "crackhead" and "junkie" who had been fighting addiction for more than 20 years.

Justice Holmes said O'Sullivan was most likely acting under the influence of methamphetamine at the time of his offending.

Mason was living with O'Sullivan at the time, while his mother lived in a seperate home. ( ABC News )

Death a result of 'extremely poor parenting'

Ms O'Gorman said O'Sullivan's lack of care in the earlier months of 2016, was a result of "extremely poor parenting and neglect" as opposed to malice toward Mason, and he did recognise the "woefulness of his behaviour".

"He is extremely remorseful for causing Mason's death," she said.

The defence said O'Sullivan was extremely remorseful for Mason's death. ( ABC News )

She also told the court O'Sullivan feared his time in prison, having already being subjected to a number of assaults in custody, including a particularly severe attack this year when he was set upon by two men with a tennis racquet, and kicked and stomped on until he was unconscious.

He suffered broken bones, bleeding to his brain and bruising to most of his body.

Justice Holmes took this into account in sentencing O'Sullivan, who received a head sentence of nine years prison and will be eligible for parole in four years.

She did not make a serious violent offence declaration because he did not have a violent criminal history and because of his "justified fear" of being assaulted again in prison.

"That will make your continued experience of imprisonment more onerous than would otherwise be the case," she said.

Charges against Mason's mother Anne-Maree Lee are still before the court. She will face a judge-only trial at a date yet to be set.