When the manager of the station, a Mr Hobbs, returned several days later and discovered the bones, he decided to report the incident, travelling 250 miles across the Liverpool Plains to Muswellbrook. The magistrate there, Captain Edward Day, reported the incident to the Colonial Secretary, Edward Thomson, who then reported it to the Governor of New South Wales, George Gipps.
Gipps didn't immediately make a decision, but by July, after being urged to do so by the Attorney-General John Plunkett, he ordered Day to take a group of mounted police to investigate. On investigating the site where the Aboriginal people were said to have been killed, They found many charred bones, with pieces of at least twenty different skulls, and other identifiable skeletal remains in numbers enough for Day to conclude that at least twenty-seven people had been killed there, three survived. Day reported back in September, after a forty-seven day investigation, having captured the eleven convicts. Fleming was not captured. The eleven convicts were charged with nine counts of murder.
Beginning on 15 November 1838, the case was heard before the Chief Justice of New South Wales, James Dowling. The convicts were represented by lawyers paid for by an association of landowners and stockmen from the Liverpool Plains region. The Black Association, as they called themselves, were led by a local magistrate, who apparently used the influence of his office to gain access to the prisoners in Sydney, where it seems he encouraged them to compile a single story and stick to it. Not one of the eleven accused gave evidence against their co-accused at the trial, something that Gipps attributes to the magistrate's role.
The station hand Anderson, the only white witness, was the key witness for the prosecution. He told the court how the twelve men had tied the victims together, and that some of the young and old were unable to walk. The shepherd also said that the son of one of the convicts had shown him a sword covered with blood. Anderson's testimony was supported by Captain Day, who had conducted the police investigation, and what forensic evidence was collected at the scene.
Justice Dowling took care to remind the jury that the law made no distinction between the murder of an Aboriginal person and the murder of a European person. The jury, after deliberating for just twenty minutes, found all eleven men not guilty. One of the jurors later told the newspaper The Australian that although he considered the men guilty of murder, he could not convict a white man of killing an Aboriginal person:
Before the men could be released from custody, however, Attorney-General Plunkett ordered that seven of the men be charged with the murder of one of the children who had been killed. The second trial was held on 29 November. Anderson, who had been the key witness at the first trial, gave an even more lucid account of the massacre at the second trial. He told the court that:
"While master was away, some men came on a Saturday, about 10; I cannot say how many days after master left; they came on horseback, armed with muskets and swords and pistols; all were armed... the blacks, when they saw the men coming, ran into our hut, and the men then, all of them, got off their horses; I asked what they were going to do with the blacks, and Russel said 'We are going to take them over the back of the range, to frighten them'."
Anderson then gave evidence that the Aboriginal people in the hut had cried out to him for assistance. He said that at least one woman was left behind in the hut "because she was good-looking, they said so," and that there was young child who had been left behind with her, who attempted to follow its mother who was tied up with the others, before Anderson carried it back to the hut.
The white men returned alone later that day, and the following morning they took firesticks from the fireplace in the hut, and later:
"I [Anderson] saw smoke in the same direction they went; this was soon after they went with the firesticks... Fleming told Kilmeister to go up by-and-by and put the logs of wood together, and be sure that all [of the remains] was consumed... the girls they left, and the two boys, and the child I sent away with 10 black fellows that went away in the morning... I did not like to keep them, as the men might come back and kill them."
Anderson said that he wanted to speak the whole truth at the second trial. He also said that he did not seek to be rewarded for testifying, rather he asked "only for protection." The trial continued until 2 am on 30 November, when the seven men were found guilty. On 5 December they were sentenced to execution by hanging. The sentence was ratified by the Executive Council of New South Wales on 7 December, with Gipps later saying in a report that no mitigating circumstances could be shown for any of the defendants, and it could not be said that any of the men were more or less guilty than the rest. The seven men were executed early on the morning of 18 December. While this was not the first time settlers were hanged for murdering Aborigines it was the first time that settlers were found guilty of, and hanged for, the killing of Aboriginal people on the frontier.
The case led to significant uproar among sections of the population and the media, sometimes voiced in favour of the perpetrators. For example, an article in the Sydney Morning Herald declared that "the whole gang of black animals are not worth the money the colonists will have to pay for printing the silly court documents on which we have already wasted too much time". The amount of publicity generated by the case may have encouraged perpetrators of similar acts to conceal evidence of their wrongdoing.
John Fleming, the leader of the massacre, was never captured, and was allegedly responsible for further massacres throughout the Liverpool Plains and New England regions. His brother. Joseph Fleming, was also linked to massacres in the Maranoa region of south-western Queensland.
John Blake, one of the four men acquitted at the first trial and not subsequently charged, committed suicide by cutting his throat in 1852. His descendants, who still live in the Inverell region, say that they like to think he did so out of a guilty conscience.
A memorial to the victims of the massacre was unveiled in 2000, consisting of a granite rock and plaque overlooking the site of the massacre. A ceremony is held each year on 10 June commemorating the victims. The memorial was vandalised in January 2005, with the words "murder", "women" and "children" chiselled off, in an attempt to make it unreadable.
The Myall Creek Massacre and Memorial Site was included on the Australian National Heritage List 7 June 2008.