The campaign has attracted criticism from widows who called it "offensive".
A McDonald's spokesperson said: "This was by no means an intention of ours."
"We wanted to highlight the role McDonald's has played in our customers' everyday lives - both in good and difficult times," the spokesperson added.
The campaign, from London-based advertising agency Leo Burnett, first aired on 12 May and is scheduled to run for seven weeks.
In the advert, the boy asks his mum about his absent dad, sparking some reminiscence.
The boy is left to wonder whether he and his father had anything in common, until he arrives at a McDonald's restaurant and orders a Filet-o-Fish and the mother says: "That was your dad's favourite too."
Bereavement charity, Grief Encounter said it had received "countless calls" from parents saying their bereaved children had been upset by the advert.
Sarah Fox's husband died two years ago. The 37-year-old from London said her seven-year-old son, who saw the advert, had only just started to understand the implications of his loss.
She said: "The advert was confusing for him and really upset him. He asked me why the boy on TV wasn't 'sad' and how he could feel happy again?
"It's an unnecessary subject to exploit for the gain of a brand."
Tania Richman, 44 from Brighton, East Sussex, said her teenage children, whose father died last year, were also "upset and offended" by the advert.
She said: "I didn't know how to handle them afterwards."
Leah Miller, 42 from London raised concerns about the lack of support advice offered after the advert.
"What are children supposed to think after watching it? That a simple meal can solve their emotional pain?
"It's irresponsible not to include any support advice or information for families affected by this issue."
The Advertising Standards Authority said it had received complaints regarding the advert, and would "carefully assess them to see whether there are grounds to investigate".
One in 29 children in the UK are bereaved of a parent or sibling by the time they are 16, according to Grief Encounter, which offers support to bereaved children and their families.
Dr Shelley Gilbert, founder and president of the charity, said: "McDonald's have attempted to speak to their audience via an emotionally driven TV campaign.
"However, what they have done is exploit childhood bereavement as a way to connect with young people and surviving parents alike - unsuccessfully.
"We fully support children and surviving parents remembering loved ones with memory boxes, family experiences which remind them of happier times and openly talking about the member of the family that has died.
"But trying to insinuate that a brand can cure all ills with one meal is insensitive and shouldn't be a way to show that a brand recognises 'the big moments in life'."
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