According to the Orca Network, J50, also known as Scarlet, was given the antibiotics via a dart as she and her pod entered US waters near the San Juan Islands on Thursday.
Sheila Thornton, lead killer whale research scientist with Fisheries and Oceans Canada, said they are anxious that the time and energy she spends carrying the body could take away from foraging or feeding.
The experimental, emergency plan to save J50 requires scientists to nail down her ailments through breath and fecal samples, then administer long-lasting antibiotics by either pole-mounted syringe or dart.
Fisheries and Oceans Canada is working with the team, and issued permits Thursday to deliver the medical treatment in Canadian waters if necessary - something that earlier had been in question.
"While very skinny and small, J50/Scarlet kept up well with her mother and siblings", NOAA stated on its website.
The Vancouver Aquarium's head veterinarian, Dr. Martin Haulena, was on the vessel assessing and treating the whale, according to statements from the aquarium and NOAA.
Canada's Department of Fisheries and Oceans stated on Twitter that it was "proud to take part in this collaborative effort to help ailing" J50.
Michael Milstein, a spokesman with NOAA Fisheries, says researchers on Wednesday spotted the 20-year-old whale known as J35 carrying her dead young off the tip of Washington's Olympic Peninsula.
Global response teams reached J Pod today in Canadian waters and followed them into USA waters near San Juan Island.
"It's not uncommon for [the whales] to split their time between the outer coast and inland waters", he said.
"This is a novel undertaking", Hanson said.
People from around the world are following the trials of the southern resident orca clan, down to only 75 animals. The scientists said they have no plans to intervene; removing the dead calf would have serious repercussions to the group.
The carcass is "surprisingly intact", she said.
Depending on the conditions, the team could gather samples and treat J50 with antibiotics on the same day, he said.
An worldwide team of experts has been waiting for an opportunity to get close to the female killer whale so they can carry out an emergency plan that includes giving her antibiotics or feeding her live salmon at sea.
The effort to save a 4-year-old orca named J50, or Scarlet, comes as another member of her family has drawn national attention for carrying her dead calf for more than two weeks, behavior interpreted by researchers to represent intense grief.
"You can look at that as mourning behaviour, there are a lot of different theories out there".