No, none that I know of; the trajectory in the Medieval period was very much towards Christianity, not away from it. Christianization was a slow process, though, so there were still non-Christian populations in Europe through the Middle Ages - the latest example I can think of are the Sami people in the Nordic countries, who were not converted until the 18th century, well past Medieval times and into the Modern era.

Now, your question specified pagan religion, which is usually meant to refer to older polytheistic, ancestral, animistic traditions, including both the Greco-Roman pantheon/mythology and other traditional tribal belief systems. But if we expand the question to include any non-Christian religions, then we do find examples of this, namely with Islam. Two major areas are worth attention here: Hispania and the Balkans.

Hispania was conquered by Muslim forces in the 8th century, and the Umayyad caliphate was established there. Muslim rule here has something of a reputation in popular imagination as an example of religious tolerance where the Muslim rulers continued to respect their Christian subjects' beliefs, and there is truth to that, as conversion was incentivized but not forced; but there were conversions to Islam by previously Christian inhabitants. By doing so, they were relieved of the jizya tax, gained better social standing, etc. A number of these did occupy prominent positions, such as local governors and military commanders. In fact, enough Christians converted to Islam that there was some concern on the part of the government about lessened tax revenue, no longer receiving their jizya. It's not quite the same as a Christian king or duke converting, but ambitious men did well for their political future by considering that choice.

The Balkans are a tricky subject indeed, and I hesitate to jump in too far; in many ways, religion is strongly linked with national and ethnic identity, and I'm not an expert in that region. Suffice to say that certain parts of the Balkans were effectively Islamized by the Ottomans, and this sometimes included nobility and political leaders. An interesting story is that of George Castrioti, also called Skanderbeg, an Albanian noble who converted to Islam served the Ottomans, then later reverted to Christianity when he deserted and became a rebel against the Ottomans.

So the broad answer to your question is no, there aren't any major examples of conversion away from Christianity by Medieval rulers, if you mean a Julian the Apostate style attempt by a leader to change his territory, but religion could be a much more fluid matter for many people in contested or border areas when it was advantageous.