NOTE: the virtually same answer was posted for a more general question "What damages does a hurting husband pay to his wife?"
Rambam Hilchos Chovel U'Mazik 4:17
וְהַמַּזִּיק אִשְׁתּוֹ בְּתַשְׁמִישׁ הַמִּטָּה חַיָּב בִּנְזָקֶיהָ:
When a person injures his wife through marital relations, he is liable for the damages.
This isn't necessarily referring to rape. However the Rambam writes in the previous halacha
Hilchos Chovel U'Mazik 4:16 :
בַּמֶּה דְּבָרִים אֲמוּרִים שֶׁחָבְלוּ בָּהּ אֲחֵרִים. אֲבָל הַבַּעַל שֶׁחָבַל בְּאִשְׁתּוֹ חַיָּב לְשַׁלֵּם לָהּ מִיָּד כָּל הַנֵּזֶק וְכָל הַבּשֶׁת וְהַצַּעַר וְהַכּל שֶׁלָּהּ וְאֵין לַבַּעַל בָּהֶן פֵּרוֹת. וְאִם רָצְתָה לִתֵּן הַדָּמִים לְאַחֵר נוֹתֶנֶת. וְכָזֶה הוֹרוּ הַגְּאוֹנִים. וְהַבַּעַל מְרַפֵּא אוֹתָהּ כְּדֶרֶךְ שֶׁמְּרַפֵּא כָּל חָלְיָהּ:
When does the above apply? When others injured her. When, however, a husband injures his wife, he is required to pay her the entire assessment for the damages, the embarrassment and the pain. This money is hers entirely. The husband has no rights to the profits. If she desires to give the money to another person, she may. This is the ruling rendered by the geonim. The husband must pay for her medical expenses, as he pays for all her other medical expenses.
Neither of these halachot from Hilchos Chovel U'Mazik explicitly address the punishment if a husband rapes his wife, but from here we can see that the husband is punished regardless.
Both of these halachos are codified by the Shulchan Aruch, Even Haezer 83:1-2