Cesare Borgia's nomination as bishop of Pamplona (at the age of 16) was ill-received for several reasons. His age was definitely a factor, but not the only one. Pamplona was a city of great symbolic importance as the ancient capital of the kingdom of Navarre. At the time, Cesare had not yet taken holy orders and had no qualification for the role other than his parentage (his father Rodrigo was the long-established Vice-Chancellor of the Church). To justify the nomination, Rodrigo praised Cesare's "merits, virtue and doctrine" and Cesare himself wrote a pastoral letter in Spanish to the clergy of Pamplona. Sarah Bradford writes that

Despite the soothing words of the Borgias, father and son, the Navarrese remained rebellious until Pope Innocent [VIII] himself was obliged to intervene with a penal admonition against those who might attempt to usurp the see of Pamplona and appropriate its revenues. (Cesare Borgia, His Life and Times, p. 23)

We don't know much of his acts as bishop (most likely because there is not much to know), although we do know he perceived the diocesan revenues through Martín Zapata, his vicar-general. Right after his nomination (autumn of 1491), Cesare started his canon law studies at the University of Pisa (he had studied in Perugia for two years already prior to this) and did not therefore set foot in Pamplona during that time. He might have after a while, if not for the death of Innocent VIII on 25 July 1492. This was the moment the Borgias had been waiting for, and they had prepared for many years for the next papal election, so Cesare's mind was evidently not set toward Pamplona in any way, shape or form from that day on.

Only twelve months after his nomination as bishop of Pamplona, he was instead named archbishop of the much wealthier Valencia.

Not one single act in the cathedral archives at Pamplona bears his signature as Bishop. (Cesare Borgia, His Life and Times, p. 282)

Ironically, when he did finally set foot in Pamplona in December 1506, at the age of 31, he was received warmly as a leader of the Navarrese independence, even though he personally did not care much for Spanish politics. Despite the Borgia family being of Spanish origins, Cesare himself had spent the vast majority of his life in Italy, and this was where his thoughts and ambitions travelled to.

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Sources: Sarah Bradford's cited book above is by far the secondary source with the most detail about Cesare's brief time as bishop of Pamplona. I also consulted other sources to corroborate the facts. Cesare's use of Martín Zapata gets a bit more explanation in Ivan Cloulas's César Borgia: Fils de pape, prince et aventurier. Rafael Sabatini, author of The Life of Cesare Borgia: A History and Some Criticisms makes no mention of Pamplona before his stay there in 1506 and says nothing of the bishopric.