Purpose: Squamous cell carcinoma (SCC) of the penis is rare. Some studies have suggested that the incidence is increasing but the available literature is equivocal. We examined the incidence of high-grade penile intraepithelial neoplasia (PeIN), the incidence and 5-year relative survival as well as mortality of penile SCC in Denmark over the latest 20 years. Methods: New cases of high-grade PeIN and penile cancer were identified from high-quality nationwide registries. Age-standardized (World) incidence rates per 100,000 person-years and average annual percentage change (AAPC) were estimated. For penile SCC, 5-year relative survival was calculated, and Cox regression was used to examine the effect of selected characteristics on mortality. Results: Altogether, 1,070 new cases of high-grade PeIN were diagnosed (1997–2018) and the incidence increased from 0.87 to 1.84 per 100,000 person-years from 1997–1998 to 2017–2018 (AAPC = 4.73; 95% CI: 3.54–5.94). We identified 1,216 penile cancer cases (1997–2018) (95.7% SCC). The incidence of penile SCC increased slightly from 0.85 per 100,000 person-years in 1997–1998 to 1.13 per 100,000 person-years in 2017–2018 (AAPC = 1.01; 95% CI: 0.24–1.79). The 5-year relative survival of penile SCC did not change substantially, whereas the mortality tended to decrease. Conclusion: Penile SCC is increasing slightly in Denmark, while a pronounced increase in the incidence of high-grade PeIN is seen. The 5-year relative survival from penile cancer was relatively stable over time. Increasing exposure to HPV infection at the population level may have contributed to the observed increase in PeIN and penile SCC. Awareness of HPV may also have contributed to the increased detection of PeIN.