Kenyatta, who handed power to his deputy before flying to The Hague, was summoned to answer questions about his floundering trial for allegedly masterminding deadly post-election violence in 2007-2008.
Wearing a charcoal suit and blue tie, a relaxed-looking Kenyatta spoke with his lawyer before the start of the "status conference".
ICC chief prosecutor Fatou Bensouda, who has alleged witness intimidation and that Nairobi is withholding evidence, was also present.
"The case is at a critical juncture, which is why I deemed appropriate to be here in person," she said.
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The repeatedly-delayed case has seen at least seven prosecution witnesses drop out, allegedly through bribes and intimidation.
Judges could decide to send the case to trial or to abandon it after the prosecution said it did not have enough evidence, although a decision is not expected on Wednesday.
A handful of demonstrators sang and danced outside the ICC ahead of Kenyatta's arrival, many of them dressed in Kenyan colours.
One large banner read: "Hands off our prez, he is innocent."
Kenyatta, 52, faces five counts at the ICC over his alleged role in orchestrating unrest in 2007 and 2008 that left 1,200 people dead and 600,000 displaced.
The Kenyan leader has appeared at the ICC before, but not since he was elected president in March 2013.
Kenyatta arrived in The Hague on Tuesday, having temporarily handed power to his deputy and erstwhile political opponent William Ruto.
Ruto is already on trial at the ICC for his part in the violence, while Kenyatta's trial has yet to begin despite a drawn-out three-and-a-half year legal saga. 1 The Kenyan leader's trial was originally scheduled to start Tuesday, but that was put off after prosecutors admitted they did not have enough evidence to proceed.