The former England paceman has been suffering from a "lower back issue", but is expected to feature in the five-match ODI series beginning next week.
Ireland play the Afghans in three T20s in India, staring on Wednesday.
"We're happy with the progress Boyd is making and feel confident that he will still make an impact on this tour," said Irish head coach John Bracewell.
"We are lucky that we have cover at present."
Bracewell added that bowler Tim Murtagh would be available for the ODI series following the birth of his second child.
The matches in Greater Noida conclude with an Intercontinental Cup encounter on 28-31 March.

A so-called Special Area of Conservation (SAC) has been created in the Inner Hebrides and Minches.
The facility is the largest conservation area for the marine species in Europe.
Scientists warned earlier this year that numbers of harbour porpoise were falling because of difficulties with catching food and breeding.
They had called on the Scottish government to act and introduce protected sites for the animals.
Environment Secretary Roseanna Cunningham said she was pleased to designate the first SAC and added: "This will help maintain the favourable conservation status and provide protection to the species and their habitats."
WWF Scotland director Lang Banks welcomed the move and said he was hopeful more such sites would be established in future.
He said: "It's fantastic news that Europe's largest Special Area of Conservation for harbour porpoise is to be located off the west coast of Scotland.
"We've long called for greater protection for this species and we look forward to working with the Scottish government and others to ensure that this site contributes to a coherent and well-managed network of marine protected areas."
Ireland bowler Boyd Rankin has been ruled out of the T20 series against Afghanistan because of a back problem.
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A new conservation area has been set up in waters off the west of Scotland to help protect harbour porpoise.