In a statement, the youth organisation said its decision to admit children and adults who identify as women does not put other female members at risk.
It follows concerns raised by a campaign group that young people are at risk of sexual abuse or getting pregnant if it continues to admit transgender people.
The case highlights the challenges youth groups face when developing transgender inclusive policies and explaining changes to staff and volunteers.
Here are some key issues youth groups should consider.
What is the scale of the issue?
Girlguiding UK changed its rules in January 2017 so that any child or young person aged from five to 25 who self-identifies as female can become a member regardless of the sex they were assigned at birth.
The Gender Identity Research and Education Society (GIRES) says this is a sensible approach as gender diversity is affecting an increasing number of people.
"The medical director for NHS England stated in June that we need to be prepared that one to three per cent of the population may wish to explore their gender, although that does not necessarily mean a medical intervention," a GIRES spokesperson explains. "Three per cent of the UK population would amount to nearly two million people, of whom about 400,000 would be under 18."
In addition, GIRES points out that the number of under-18s being referred to specialist gender identity services has risen by 50 per cent a year for the past five years.
What legislation is it governed by?
An individual's expression of their gender identity should be respected in accordance with the Equality Act 2010. This requires organisations to consider how to provide gender-specific facilities such as toilets, showers and sleeping accommodation.
The act requires organisations to ensure the privacy of a transgender person is respected.
When a person is 18 or over, it is unlawful to tell other people that they are transgender unless the person has given permission, and it is good practice to maintain confidentiality for under-18s.
Advice on the Girlguiding UK website states that if a person feels that telling others would help support the transgender young person, they should be consulted.
A campaign group supporting the two ex-volunteers has called on Girlguiding UK to review the policy and be more transparent. The group says parents should be told if a transgender young person is sharing bedrooms and bathrooms with their children.
What practical steps can be taken?
There are measures youth groups should consider taking to ensure activities and trips are inclusive for transgender young people, according to Joey McKillop, who has published advice for youth groups on the GIRES website.
Swimming is potentially problematic, because the use of gendered changing rooms leaves a transgender person feeling uncomfortable and vulnerable to assault, McKillop writes.
Girlguiding UK's advice is that groups should plan activities carefully and for transgender young people to know in advance so they can make an informed decision whether to participate.
"If the young person is unsure, discuss with them what they would like to do as an alternative," it says.
McKillop says residential trips need careful planning so that the transgender young person is accommodated alongside the most suitable individuals and in a way that protects the dignity and privacy of everyone.
Where a transgender young person feels uncomfortable sharing accommodation, alternative options should be provided in a discreet way, says Girlguiding UK.
How can staff be supported?
GIRES says that in addition to developing transgender-inclusive policies, youth groups should consider the training needs of staff and volunteers.
It has developed a free three-part e-learning course that includes an introduction to gender identities and addresses misconceptions. It also outlines how to create supportive environments for young gender variant people, including in education settings, and the treatment options available and mental health issues that can arise.
GIRES advises youth groups to display posters that promote respect for gender diversity and other characteristics protected by equality law and arrange events during LGBT history month in February, the transgender day of visibility on 31 March and trans-pride Brighton in June.
