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.
Ireland bowler Boyd Rankin has been ruled out of the T20 series against Afghanistan because of a back problem.