Coroner Jim Kitson said the inquest into the death of 11-year-old Francis Rowntree in 1972 would be "severely hampered" if he could not attend.
He said the man's heart condition had to be a factor when deciding whether to compel him to give evidence.
The coroner told the preliminary hearing it was a "fine balancing act".
Francis was playing with friends at the Divis Flats complex off the Falls Road in west Belfast in April 1972 when he was struck on the head by the rubber bullet. He died in hospital several days later.
Controversy surrounds the shooting, with disputed claims about whether the young boy was struck directly or hit by a ricochet, and if the bullet had been doctored to make it potentially cause more injury.
The former Royal Anglian Regiment member who fired the rubber bullet is known to the court as soldier B.
A barrister for the Ministry of Defence told the hearing that soldier B's consultant cardiologist had expressed "significant reservations" about his fitness to attend, in a report produced for the coroner's court.
"It appears on the face of it to be quite a severe condition involving multiple medical interventions over the years," the lawyer said.
He added: "The likelihood of a heart attack or death would be small but not zero.
"There is a significant risk to the health of this man to compel him to give evidence."
A barrister representing the Rowntree family said a number of steps could be taken to make the witness feel at ease.
She suggested the former soldier could give evidence via video-link; there could be regular breaks in the hearing; medical assistance could be on standby and the court could be partially cleared.
She told the coroner: "You know the gravity of the case and you know he's essentially the key witness and very important to the case."
Mr Kitson said: "This is a key witness and clearly the inquest would be severely hampered if this witness is not in attendance, but I'm acutely aware of the impact on this man's health.
"It's a fine balancing act between the two prerogatives and pressures - I will reflect on this very carefully."
The inquest is due to begin on 27 April.

Ackerman was initially banned in October last year after being found guilty of corruption.
He had laid bets against a horse knowing its jockey aimed not to win.
Ackerman was granted a stay of implementation in November, but his disqualification has been reactivated with immediate effect until 11 June.
However, his fine of £5,000 was quashed upon appeal, at the invitation of the British Horseracing Authority.
Ackerman was banned after an investigation into six races featuring Ad Vitam at Kempton and Wolverhampton between 2 November, 2011 and 8 March, 2012.
He was found to have breached the rules of racing alongside jockey Michael Stainton, registered owner Kenneth Mackay and former owner David Greenwood.
Stainton was banned for two years, Mackay for six months and fined £5,000, with Greenwood, who had already been warned off for a separate offence, banned for eight years. All three also failed in their appeals, although, a separate appeal by Stainton against the penalty imposed "will be considered in due course".
Stewart-Moore Solicitors, who represent Ackerman, Greenwood and Mackay, said in a statement that the "matter needs to be resolved by a High Court judge".
"Messrs Ackerman, Greenwood and Mackay have not acted in breach of the rules of racing in any way," they added.
"In spite of this they have been found, yet again, to have taken part in a conspiracy that has never been properly put to them."
A coroner has said he will reflect carefully on whether a soldier who fired a rubber bullet that killed a boy is too ill to give evidence.
[NEXT_CONCEPT]
Towcester racecourse chief executive Kevin Ackerman has failed in his bid to overturn a six-month suspension from racing.