Purpose: RayStation treatment planning system employs pencil beam (PB) and Monte Carlo (MC) algorithms for proton dose calculations. The purpose of this study is to evaluate the radiobiological and dosimetric impact of RayStation PB and MC algorithms on the intensity-modulated proton therapy (IMPT) breast plans. Methods: The current study included ten breast cancer patients, and each patient was treated with 1–2 proton beams to the whole breast/chestwall (CW) and regional lymph nodes in 28 fractions for a total dose of 50.4 Gy relative biological effectiveness (RBE). A total clinical target volume (CTV_Total) was generated by combining individual CTVs: AxI, AxII, AxIII, CW, IMN, and SCVN. All beams in the study were treated with a range shifter (7.5 cm water equivalent thickness). For each patient, three sets of plans were generated: (a) PB optimization followed by PB dose calculation (PB-PB), (b) PB optimization followed by MC dose calculation (PB-MC), and (c) MC optimization followed by MC dose calculation (MC-MC). For a given patient, each plan was robustly optimized on the CTVs with same parameters and objectives. Treatment plans were evaluated using dosimetric and radiobiological indices (equivalent uniform dose (EUD), tumor control probability (TCP), and normal tissue complication probability (NTCP)). Results: The results are averaged over ten breast cancer patients. In comparison to PB-PB plans, PB-MC plans showed a reduction in CTV target dose by 5.3% for D99% and 4.1% for D95%, as well as a reduction in TCP by 1.5–2.1%. Similarly, PB overestimated the EUD of target volumes by 1.8─3.2 Gy(RBE). In contrast, MC-MC plans achieved similar dosimetric and radiobiological (EUD and TCP) results as the ones in PB-PB plans. A selection of one dose calculation algorithm over another did not produce any noticeable differences in the NTCP of the heart, lung, and skin. Conclusion: If MC is more accurate than PB as reported in the literature, dosimetric and radiobiological results from the current study suggest that PB overestimates the target dose, EUD, and TCP for IMPT breast cancer treatment. The overestimation of dosimetric and radiobiological results of the target volume by PB needs to be further interpreted in terms of clinical outcome. © 2019 The Authors. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.