Company: CYTK
Filing Date: 2025-02-27
Form Type: S-3ASR
Source: 0001193125-25-039426
Chunk: 1

Company: CYTOKINETICS INC
Filing Date: 2025-02-27
Form: S-3ASR
Chunk 1
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 Act, check the following box. ☒ If this Form is a post-effective amendment to a registration statement filed pursuant to General Instruction I.D. filed to register additional securities or additional classes of securities pursuant to Rule 413(b) under the Securities Act, check the following box. ☐ Indicate by check mark whether the Registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer,a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2of the Exchange Act:

| Large accelerated filer |     | ☒ |     | Accelerated filer         |     | ☐ |
| Non-accelerated filer   |     | ☐ |     | Smaller reporting company |     | ☐ |
| Emerging growth company |     | ☐ |     |                           |     |   |

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 7(a)(2)(B) of the Securities Act. ☐

EXPLANATORY NOTE This registration statement contains the following documents:

| • |     | a base prospectus which covers the offering, issuance and sale by us of an indeterminate amount of common stock, 
 preferred stock, debt securities and/or warrants, in each case from time to time in one or more offerings; and   |

| • |     | a sales agreement prospectus supplement covering the offering, issuance and sale by us of up to a maximum                                                                      
 aggregate offering price of $500.0 million of our common stock that may be issued and sold under an Open Market Sale AgreementSM, dated February 27, 2025, with Jefferies LLC. |

The base prospectus immediately follows this explanatory note. The specific terms of any securities to be offered pursuant to the base prospectus other than the shares under the Sales Agreement will be specified in a prospectus supplement to the base prospectus. The specific terms of the securities to be issued and sold under the Sales Agreement are specified in the sales agreement prospectus supplement that immediately follows the base prospectus.

PROSPECTUS

Common Stock

Preferred Stock

Debt Securities

Warrants

From time to
time, Cytokinetics Incorporated or selling securityholders may offer