In February, the Blues were banned from signing players for their men's teams for the next two transfer windows after being found guilty by FIFA's disciplinary committee of breaching regulations relating to the recruitment of minors.
Chelsea denied any wrongdoing and appealed. On Wednesday, the governing body of world soccer announced that its appeal committee had "decided to partially uphold the appeal".
The committee lifted part of the ban, but only for players under 16 who are not "international transfers and first registrations of foreign minor players".
That means Chelsea will still not be able to sign male players over the age of 16 when the summer transfer window opens.
Chelsea had been eager to have the ban lifted, or suspended pending the appeal, so they could be in a position to sign a replacement for Belgium Eden Hazard, who is being touted as a possible £100 million (116 million euros, $131 million) transfer target for Real Madrid.
The appeal committee also confirmed the fine of 600,000 Swiss francs (526,000 euros, $590.000).