The agreement establishes a community liaison group to oversee both long-term and day-to-day operational matters.
This includes operating hours, traffic management and the number of social service agencies operating at the facility once it is built.
The agreement also reduced the number of large events to be held on-site.
VNA spokesperson Marjorie Manthei said its objection to the Youth Hub's application focused on the impact of the facility's non-residential activities on a small residential neighbourhood.
"The purpose of the conditions we all agreed to is to ensure both groups can now operate as good neighbours.
"We have mitigated as many of the potential effects on residential amenity as we could".
Youth Hub Trust chair Dame Sue Bagshaw said they were thrilled with the news.
"This agreement means resource consent has now been achieved, enabling us to work together, hand in hand, to ensure that the Youth Hub delivers not only for the city's young people in need, but also, importantly, the local neighbourhood.
"We are deeply appreciative of the VNA's approach to mediation and we are committed to working with them to ensure an open, constructive and harmonious relationship."
Manthei, representing 125 VNA members, said she agreed that the mediation outcome has provided a pathway to an effective partnership.
"Of course we're disappointed that this large piece of residential land won't be used only for housing.
"However mediation allowed us all to take another look at the plans and find positive, workable compromises."
Bagshaw said they had to make some adjustments to their original plans to facilitate the agreement.
"It is extremely important to us that the Youth Hub assimilates seamlessly into this wonderful, inclusive, city neighbourhood. We see the Hub and its young clients, onsite and support staff as contributing to the positivity and kaitiakitanga of this neighbourhood, adding a young people's voice and a sense of empathy, positivity and co-operation."
She said once built, the youth hub, Te Hurihanga Ō Rangatahi, will be a communal place of growth, support and wellbeing for 10-25-year-olds, providing support services including access to catch-up education, healthcare, mental health counselling, vocational training, recreation and employment.
"Uniquely, the development will provide onsite, purpose-built accommodation for up to 40 young people aged 16-24 years, in need. Most will stay from 3-18 months at a time, providing they are involved in formal education or actively looking for work."
"We hope they will transition from the planned shared hostel rooms into our 3-bedroom townhouses, where they'll be given mental and social support from qualified, live-in residential staff. They'll learn cooking, cleaning and social living skills to help them progress to a future independant flatting environment."
The hub will provide space for about 12 different youth organisations including 298 Health Centre, YouthLine, Qtopia and the Christchurch City Mission, providing a one-stop-shop for essential services.
The acre of land on Salisbury St was specifically purchased for the project by Anglican Care and will be leased back to the Youth Hub Trust to build and run the facility.
Bagshaw said the next aim is to raise the $15 million shortfall in funds to get the hub built.
The project received a much-needed boost last year – a $10 million dollar kick-start from the Government's Covid-19 Response and Recovery Fund, set aside for shovel-ready projects.