Background Research on penile cancer (PeCa) is predominantly conducted in countries with centralized treatment of PeCa-patients. In Germany and Austria (G + A), no state-regulated centralization is established, and no information is available on how PeCa-research is organized. Methods Current research competence in PeCa was assessed by a 36-item questionnaire sent to all chairholders of urological academic centers in G + A. Based on PubMed records, all scientific PeCa-articles of 2012–2022 from G + A were identified. Current research trends were assessed by dividing the literature search into two periods (P1: 2012–2017, P2: 2018–2022). A bibliometric analysis was supplemented. Results Response rate of the questionnaire was 75%, a median of 13 (IQR: 9–26) PeCa-patients/center was observed in 2021. Retrospective case series were conducted by 38.9% of participating clinics, while involvement in randomized-controlled trials was stated in 8.3% and in basic/fundamental research in 19.4%. 77.8% declared an interest in future multicenter projects. 205 PeCa-articles were identified median impact factor: 2.77 (IQR: 0.90–4.37). Compared to P1, P2 showed a significant increase in the median annual publication count (29 (IQR: 13–17) vs. 15 (IQR: 19–29), p  < 0.001), in multicenter studies (79.1% vs. 63.6%, p  = 0.018), and in multinational studies (53% vs. 28.9%, p  < 0.001); the proportion of basic/fundamental research articles significantly declined (16.5% vs. 28.9%, p  = 0.041). Four of the top-5 institutions publishing PeCa-articles are academic centers. Bibliometric analyses revealed author networks, primary research areas in PeCa, and dominant journals for publications. Conclusions Given the lack of centralization in G + A, this analysis highlights the need for research coordination within multicenter PeCa-projects. The decline in basic/fundamental research should be effectively addressed by the allocation of funded research projects.