The Bulgarian thinks the forward's international duties are affecting his form, while he was not impressed with Real Madrid in the Clasico.
The 26-year-old has been struggling to find his best form ever since returning from injury and has not found the net in his last three Liga games, including Tuesday's 3-0 win over Celta.
Head coach Gerardo Martino stated last week that he's not worried about Messi, but Stoichkov thinks fatigue is affecting the prolific attacker's form.
"I think that Messi's not at his best, because he's played and traveled with his national side a lot," Stoichkov told Onda Cero.
The Bulgarian also briefly reflected on Barcelona's 2-1 win over Real Madrid at the weekend and was not impressed with the Santiago Bernabeu side's creative drought.
"I saw a Madrid side that was bullish but lacking in ideas for most of the game."