Commissioner Wally Oppal ruled in a written statement this week that the woman's annonymity will be protected, but other provisions of the inquiry's vulnerable witness protection protocol won't apply.
Oppal concluded she must give her testimony in person, not through an affidavit, and undergo cross-examination.
"I emphasize that evidence that has not been subject to cross-examination cannot be used to substantiate findings of misconduct or uncorroborated findings of fact," wrote Oppal.
That's because what she has to say could be central to the inquiry's mandate of discovering why Pickton wasn't caught sooner, Oppal said.
One of Oppal's terms of reference is to inquire into and make findings of fact about the Jan. 27, 1998 decision by B.C.'s Criminal Justice Branch to stay charges of attempted murder, assault with a weapon, forcible confinement and aggravated assault against Pickton.
During Pickton's preliminary hearing, the woman, identified at the inquiry as Person X, testified that Pickton attacked her in 1997.
She said Pickton picked her up on a street corner on Vancouver's Downtown Eastside and took her to his Port Coquitlam farm for sex.
She testified after sex, Pickton came up behind her, caressed her left hand and then slapped a handcuff on it.
They began fighting and she testified she slashed Pickton across the throat and she was also stabbed before the fight continued outside.
She eventually was able to escape and flagged down a passing car.
Pickton was charged with attempted murder and aggravated assault and released on $2,000 bail.
Those charges were stayed in January 1998 because there was not a reasonable likelihood of securing a conviction in the case, said a spokesman at the time.
The woman did not testify at Pickton's trial and her story was not made public until after Pickton was convicted.
Critics have suggested that if the case had gone to trial and Pickton had been convicted, his murder spree would have been cut short and lives would have been saved.
Though he claimed he killed 49, a jury convicted Pickton of six counts of second-degree murder in December 2007, and in July 2010, the Supreme Court of Canada upheld that conviction.
Oppal's ruling follows an application by several lawyers at the beginning of November.
Jason Gratl, a lawyer who was appointed to represent the broad interests of the Downtown Eastside, asked Oppal for a publication ban protecting the identities of vulnerable witnesses called to testify at the inquiry.
Vulnerable witnesses include current or former sex-trade workers in the Downtown Eastside and victims of sexual assault.
He also asked the commission to allow vulnerable witnesses to submit testimony through affidavit and avoid cross-examination.
Lawyers for the RCMP, the Vancouver Police Department and the Vancouver Police Board did not oppose Gratl's application on the publication ban or of evidence being submitted by affidavits.
But they did take issue with any "blanket order" and argued issues should be decided on a case-by-case basis.
The Criminal Justice Branch also argued the vulnerable witness protection protocol should not apply to Person X.
In his written ruling, Oppal concluded aboriginal women are also particularly vulnerable and are not likely to testify unless "special considerations are given to them."
"In my view, nothing short of strong, clear proactive protection measures sought in this application will facilitate vulnerable witnesses to provide their evidence to the commission," he wrote.
Oppal ruled vulnerable witnesses will be protected by the protocol unless an inquiry participant applies to limit the measures in a specific case.
Note to readers: This is a corrected version. A previous story wrongly said Jason Gratl was a lawyer for the woman.