Justice Harrison was made a Queen's Counsel in 1994 and appointed as a High Court judge in 2001, before taking up his current position in 2010.
But on July 15, 2013, he found his ANZ account $42,259 lighter than it should have been.
Court documents were released to NZME. but a judge ruled that the way Stewart drained the money could not be published until after sentencing.
The defendant was due to be sentenced earlier this year, but the hearing was deferred to another date to assess the possibility of a restorative justice conference.
It could have pitted the judge against Stewart in an over-the-table, supervised conversation but it was later deemed unsuitable for such a meeting.
The stolen funds represent about 10 per cent of the victim's salary.
Judicial salaries and allowances as of October 2012 put a Court of Appeal judge's yearly wage at $415,000. A ministry spokesman said the judge was not keen to discuss the case.
"Justice Harrison advises me he is unable to comment publicly on the sentencing process," the spokesman said.
During his career as a judge, Justice Harrison has presided over dozens of fraud cases, many more serious than the one in which he became a victim.
In 2009, former All Black Doug Rollerson was convicted but freed without penalty by Justice Harrison for his part in a complex scam which cheated sports organisations out of charity money.
The judge said there was no point imposing a fine because the defendant had not profited from the crime.
Justice Harrison also presided over the case of Colleen Margaret Gray, 66, and Bruce Kenneth Gray, 65, who siphoned $30,000 from a decile-one school in Otara.
The couple appealed their home detention sentences last year, but abandoned the appeal when the judge warned them they might end up behind bars.
Stewart will also be sentenced on other charges after stealing a car at the end of September 2013. Police later found him with drugs and drug paraphernalia in the car and laid further charges on which he will also be sentenced later this month.
It is understood the defendant has previous convictions and he made the news in 2003 as a teenager when he climbed the roof of a Napier church during a drunken escapade.
He told the court he had been taking a shortcut home and ended up climbing a drainpipe onto the roof of the Methodist Trinity Church. Stewart kicked a fire escape door, smashing a glass panel window, and was jailed for six weeks and fined $172.
He faces a maximum jail term of seven years on the fraud charges.